The TCI Biorepository and Pathology Shared Resource (BPSR) integrates biorepository, histology, immunostaining, and molecular services in support of basic, clinical, epidemiologic, and translational cancer research throughout the TCI community. Biopsy and surgical specimens are processed, banked, and distributed to investigators as fresh, frozen, fixed, or procured according to investigator specifications. The BPSR hosts a suite of advanced pathology services including diverse staining, imaging, and quantitative digital image analyses, along with macromolecule extraction for subsequent investigations. Liquid biospecimen processing and management support TCI research programs and clinical trials. Finally, the BPSR is a multi-dimensional group providing consultation, education, technical support, and training for basic science, translational, and clinical cancer researchers across the Mount Sinai Health System.

Recent Publications

• Rodilla AM, Valanparambil RM, Mack PC, Hsu CY, Cagan J, Tavolacci SC, Carreño JM, Brody R, Moore A, King JC, Gomez JE, Rohs N, Rolfo C, Bunn PA Jr, Gerber DE, Minna JD, Krammer F, Ramalingam SS, García-Sastre A, Shyr Y, Ahmed R, Hirsch FR. Longitudinal nucleocapsid antibody testing reveals undocumented SARS-CoV-2 infections in patients with lung cancer. Cancer Cell 2023 41(11): 1838-1840. Read more
• Galsky MD, Daneshmand S, Izadmehr S, Gonzalez-Kozlova E, Chan KG, Lewis S, Achkar BE, Dorff TB, Cetnar JP, Neil BO, D'Souza A, Mamtani R, Kyriakopoulos C, Jun T, Gogerly-Moragoda M, Brody R, Xie H, Nie K, Kelly G, Horowitz A, Kinoshita Y, Ellis E, Nose Y, Ioannou G, Cabal R, Del Valle DM, Haines GK, Wang L, Mouw KW, Samstein RM, Mehrazin R, Bhardwaj N, Yu M, Zhao Q, Kim-Schulze S, Sebra R, Zhu J, Gnjatic S, Sfakianos J, Pal SK. Gemcitabine and cisplatin plus nivolumab as organ-sparing treatment for muscle-invasive bladder cancer: a phase 2 trial. Nat Med 2023 29(11):2825-2834. Read more
• Sattiraju A, Kang S, Giotti B, Chen Z, Marallano VJ, Brusco C, Ramakrishnan A, Shen L, Tsankov AM, Hambardzumyan D, Friedel RH, Zou H. Hypoxic niches attract and sequester tumor-associated macrophages and cytotoxic T cells and reprogram them for immunosuppression. Immunity 2023 56(8):1825-1843.e6. Read more
• Magen A, Hamon P, Fiaschi N, Soong BY, Park MD, Mattiuz R, Humblin E, Troncoso L, D'souza D, Dawson T, Kim J, Hamel S, Buckup M, Chang C, Tabachnikova A, Schwartz H, Malissen N, Lavin Y, Soares-Schanoski A, Giotti B, Hegde S, Ioannou G, Gonzalez-Kozlova E, Hennequin C, Le Berichel J, Zhao Z, Ward SC, Fiel I, Kou B, Dobosz M, Li L, Adler C, Ni M, Wei Y, Wang W, Atwal GS, Kundu K, Cygan KJ, Tsankov AM, Rahman A, Price C, Fernandez N, He J, Gupta NT, Kim-Schulze S, Gnjatic S, Kenigsberg E, Deering RP, Schwartz M, Marron TU, Thurston G, Kamphorst AO, Merad M. Intratumoral dendritic cell-CD4+ T helper cell niches enable CD8+ T cell differentiation following PD-1 blockade in hepatocellular carcinoma. Nat Med 2023 29(6):1389-1399. Read more
• Park MD, Reyes-Torres I, LeBerichel J, Hamon P, LaMarche NM, Hegde S, Belabed M, Troncoso L, Grout JA, Magen A, Humblin E, Nair A, Molgora M, Hou J, Newman JH, Farkas AM, Leader AM, Dawson T, D'Souza D, Hamel S, Sanchez-Paulete AR, Maier B, Bhardwaj N, Martin JC, Kamphorst AO, Kenigsberg E, Casanova-Acebes M, Horowitz A, Brown BD, De Andrade LF, Colonna M, Marron TU, Merad M. TREM2 macrophages drive NK cell paucity and dysfunction in lung cancer. Nat Immunol 2023 24(5):792-801. Read more

Location

Annenberg Building, Room 15-05
1468 Madison Avenue
Box 1194
New York, NY 10029

Contact
Rachel Brody, MD, PhD
Director, Institutional Biorepository
rachel.brody@mountsinai.org

Directors: Madhu Mazumdar, PhD  and Marcio Diniz, PhD

The TCI Biostatistics Shared Resource (BSR) collaborates with TCI members on designing laboratory experiments, population studies, and clinical trials. The BSR determines optimal group sizes and drafts high-quality statistical analysis plans to ensure rigor and reproducibility. The BSR provides biostatisticians with expertise in comprehensive coverage of analytic methodologies, including software programming, table creation, and data visualization; they translate these components into language understandable by the scientific community, andsupport manuscript preparation and grant proposals. Training on all quantitative data science disciplines is available through seminars, walk-in clinics, and workshops.

Director: Robert Sebra, PhD

The TCI Cancer Genomics Technologies Shared Resource (CGTSR) facilitates scientific, translational, and clinical breakthroughs by harnessing cutting-edge molecular -omics techniques, advanced instrumentation, and computational methods. The CGTSR offers TCI members the latest developments in bulk, single-cell, spatial, and in-situ multi-omics data generation platforms; while also providing expertise to optimize experimental design, data quality, affordability, and access. The team is composed of 29 staff and faculty housed in the Mount Sinai Discovery and Innovation Center, which includes instrumentation, molecular and cell biology spaces, and BSL2/BSL2+ laboratories. Post-sequencing data analyses are performed using the secured and centralized Mount Sinai High-Performance Computing facility with 1.5 Petabyte storage capacity. The CGTSR maintains a comprehensive suite of genomics services that accelerates cancer discovery, inter- and intra-programmatic collaborations within the TCI community, and benchmarks new technologies to continually match the evolving needs of TCI members.

Recent Publications

• Torre D, Fstkchyan YS, Ho JSY, Cheon Y, Patel RS, Degrace EJ, Mzoughi S, Schwarz M, Mohammed K, Seo JS, Romero-Bueno R, Demircioglu D, Hasson D, Tang W, Mahajani SU, Campisi L, Zheng S, Song WS, Wang YC, Shah H, Francoeur N, Soto J, Salfati Z, Weirauch MT, Warburton P, Beaumont K, Smith ML, Mulder L, Villalta SA, Kessenbrock K, Jang C, Lee D, De Rubeis S, Cobos I, Tam O, Hammell MG, Seldin M, Shi Y, Basu U, Sebastiano V, Byun M, Sebra R, Rosenberg BR, Benner C, Guccione E, Marazzi I. Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Mol Cell 2023; 83(32):4255-4271.e9. Read more
• Chen Z, Giotti B, Kaluzova M, Vallcorba MP, Rawat K, Price G, Herting CJ, Pinero G, Cristea S, Ross JL, Ackley J, Maximov V, Szulzewsky F, Thomason W, Marquez-Ropero M, Angione A, Nichols N, Tsankova NM, Michor F, Shayakhmetov DM, Gutmann DH, Tsankov AM, Hambardzumyan D. A paracrine circuit of IL-1β/IL-1R1 between myeloid and tumor cells drives genotype-dependent glioblastoma progression. J Clin Invest 2023; 133(22):e163802. Read more
• Galsky MD, Daneshmand S, Izadmehr S, Gonzalez-Kozlova E, Chan KG, Lewis S, Achkar BE, Dorff TB, Cetnar JP, Neil BO, D'Souza A, Mamtani R, Kyriakopoulos C, Jun T, Gogerly-Moragoda M, Brody R, Xie H, Nie K, Kelly G, Horowitz A, Kinoshita Y, Ellis E, Nose Y, Ioannou G, Cabal R, Del Valle DM, Haines GK, Wang L, Mouw KW, Samstein RM, Mehrazin R, Bhardwaj N, Yu M, Zhao Q, Kim-Schulze S, Sebra R, Zhu J, Gnjatic S, Sfakianos J, Pal SK. Gemcitabine and cisplatin plus nivolumab as organ-sparing treatment for muscle-invasive bladder cancer: a phase 2 trial. Nat Med 2023;29(11):2825-2834. Read more
• Torre D, Francoeur NJ, Kalma Y, Gross Carmel I, Melo BS, Deikus G, Allette K, Flohr R, Fridrikh M, Vlachos K, Madrid K, Shah H, Wang YC, Sridhar SH, Smith ML, Eliyahu E, Azem F, Amir H, Mayshar Y, Marazzi I, Guccione E, Schadt E, Ben-Yosef D, Sebra R. Isoform-resolved transcriptome of the human preimplantation embryo. Nat Commun 2023; 14(1):6902. Read more
• Coffey DG, Maura F, Gonzalez-Kozlova E, Diaz-Mejia JJ, Luo P, Zhang Y, Xu Y, Warren EH, Dawson T, Lee B, Xie H, Smith E, Ciardiello A, Cho HJ, Rahman A, Kim-Schulze S, Diamond B, Lesokhin A, Kazandjian D, Pugh TJ, Green DJ, Gnjatic S, Landgren O. Immunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma. Nat Commun 2023; 14(1): 5335. Read more

Location

787 11th Ave
Open Lab Rm 800
New York, NY 10019

Contact

Robert Sebra, PhD
Director, Technology Development
robert.sebra@mssm.edu

Director: Jordi Ochando, PhD

The TCI Flow Cytometry Shared Resource (FCSR) provides access to modern technologies, services, and expertise in flow cytometry to enhance scientific discovery and collaboration within the TCI community. The FCSR proactively monitors and introduces new flow cytometry equipment, methods, and data analyses approaches to promote impactful studies and align with the cancer center’s expanding needs. The FCSR maintains cancer-focused personnel and contributes to TCI’s research mission by providing consultation, priority access, education, and cost-effectiveness.

Recent Publications

• Wilk CM, Cathomas F, Török O, Le Berichel J, Park MD, Bigenwald C, Heaton GR, Hamon P, Troncoso L, Scull BP, Dangoor D, Silvin A, Fleischmann R, Belabed M, Lin H, Merad Taouli E, Boettcher S, Li L, Aubry A, Manz MG, Kofler JK, Yue Z, Lira SA, Ginhoux F, Crary JF, McClain KL, Picarsic JL, Russo SJ, Allen CE, Merad M. Circulating senescent myeloid cells infiltrate the brain and cause neurodegeneration in histiocytic disorders. Immunity 2023; 56(12):2790-2802.e6. Read more
• Aleman A, van Kesteren M, Zajdman AK, Srivastava K, Cognigni C, Mischka J, Chen LY, Upadhyaya B, Serebryakova K, Nardulli JR, Lyttle N, Kappes K, Jackson H, Gleason CR, Oostenink A, Cai GY, Van Oekelen O; PVI/MM/Seronet Study Group; van Bakel H, Sordillo EM, Cordon-Cardo C, Merad M, Jagannath S, Wajnberg A, Simon V, Parekh S. Cellular mechanisms associated with sub-optimal immune responses to SARS-CoV-2 bivalent booster vaccination in patients with Multiple Myeloma. EBioMedicine 2023; 98:104886. Read more
• Chen Z, Giotti B, Kaluzova M, Vallcorba MP, Rawat K, Price G, Herting CJ, Pinero G, Cristea S, Ross JL, Ackley J, Maximov V, Szulzewsky F, Thomason W, Marquez-Ropero M, Angione A, Nichols N, Tsankova NM, Michor F, Shayakhmetov DM, Gutmann DH, Tsankov AM, Hambardzumyan D. A paracrine circuit of IL-1β/IL-1R1 between myeloid and tumor cells drives genotype-dependent glioblastoma progression. J Clin Invest 2023; 133(22):e163802. Read more
• Filipescu D, Carcamo S, Agarwal A, Tung N, Humblin É, Goldberg MS, Vyas NS, Beaumont KG, Demircioglu D, Sridhar S, Ghiraldini FG, Capparelli C, Aplin AE, Salmon H, Sebra R, Kamphorst AO, Merad M, Hasson D, Bernstein E. MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping. Nat Cell Biol 2023; 25(9):1332-1345. Read more
• Sattiraju A, Kang S, Giotti B, Chen Z, Marallano VJ, Brusco C, Ramakrishnan A, Shen L, Tsankov AM, Hambardzumyan D, Friedel RH, Zou H. Hypoxic niches attract and sequester tumor-associated macrophages and cytotoxic T cells and reprogram them for immunosuppression. Immunity 2023; 56(8):1825-1843.e6. Read more

Locations

Icahn Building IMI 13-05 Analyzers
Tel: 212-659-9440

Icahn Building IMI 13-52a Sorters
Tel: 212-659-8201

Icahn Building IMI 13-72 Sorters
Tel: 212-659-9439

Hess Building CSM S5-304 Sorter
Tel: 212-824-9596

Hess Building CSM S6-308 Sorter
Tel: 212-824-9595 

Contact

Jordi Ochando, PhD
Scientific Director
jordi.ochando@mssm.edu

Director: Deanna Benson, PhD

The TCI Microscopy and Advanced Bioimaging Shared Resource (MABSR) manages cutting-edge instrumentation and imaging strategies for the cancer community. The MABSR provides access, expertise, and consulting services for state-of-the-art super-resolution, light-sheet microscopy, and electron microscopy, as well as confocal, multi-photon, and widefield microscopes. With TCI-focused staff, the MABSR collaborates with TCI members to develop advanced image analyses strategies and pipelines, and integrate new equipment and technologies based on TCI needs.The MABSR offers complete imaging support from consultation, sample preparation, microscope training, staff-assisted data capture, and high-performance computing workstations for image analysis. In addition, a strong commitment to education is supported by participation in numerous campus-based and national initiatives, along with co-directing an annual graduate-level microscopy course.

Recent Publications

• Krause GJ, Kirchner P, Stiller B, Morozova K, Diaz A, Chen KH, Krogan NJ, Agullo-Pascual E, Clement CC, Lindenau K, Swaney DL, Dilipkumar S, Bravo-Cordero JJ, Santambrogio L, Cuervo AM. Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy. Cell Rep 2023; 42(12):113529. Read more
• Wilk CM, Cathomas F, Török O, Le Berichel J, Park MD, Bigenwald C, Heaton GR, Hamon P, Troncoso L, Scull BP, Dangoor D, Silvin A, Fleischmann R, Belabed M, Lin H, Merad Taouli E, Boettcher S, Li L, Aubry A, Manz MG, Kofler JK, Yue Z, Lira SA, Ginhoux F, Crary JF, McClain KL, Picarsic JL, Russo SJ, Allen CE, Merad M. Circulating senescent myeloid cells infiltrate the brain and cause neurodegeneration in histiocytic disorders. Immunity 2023; 56(12):2790-2802.e6. Read more
• Liang R, Lin M, Menon V, Qiu J, Menon A, Breda L, Arif T, Rivella S, Ghaffari S. Elevated CDKN1A (P21) mediates β-thalassemia erythroid apoptosis, but its loss does not improve β-thalassemic erythropoiesis. Blood Adv 2023; 7(22):6873-6885. Read more
• Weber M, Nguyen MB, Li MY, Flora P, Shuda M, Ezhkova E. Merkel Cell Polyomavirus T Antigen-Mediated Reprogramming in Adult Merkel Cell Progenitors. J Invest Dermatol 2023; 143(11): 2163-2176.e6. Read more
• Filipescu D, Carcamo S, Agarwal A, Tung N, Humblin É, Goldberg MS, Vyas NS, Beaumont KG, Demircioglu D, Sridhar S, Ghiraldini FG, Capparelli C, Aplin AE, Salmon H, Sebra R, Kamphorst AO, Merad M, Hasson D, Bernstein E. MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping. Nat Cell Biol 2023; 25(9):1332-1345. Read more

Location
1468 Madison Avenue
Room 18-250
New York, NY 10029

Contact
Deanna Benson, PhD
Scientific Director
deanna.benson@mssm.edu

Directors: Miriam Merad, MD, PhD and Sacha Gnjatic, PhD

The TCI Human Immune Monitoring Center Shared Resource (HIMCSR) is a collaborative consortium of technologists, immunologists, clinicians, and computational biologists with the coordinated goal of generating unprecedented immune profiling datasets to interrogate the etiology of cancer, novel biomarkers of disease course, and response to immunotherapy trials in cancer patients. The HIMCSR includes a range of cutting-edge high-throughput technology platforms to define circulating immune factors in blood and body fluids; characterize immune cells in blood, bone marrow and tissue samples; interrogate specific cellular, molecular immune

pathways that may be dysregulated in disease; and characterize changes upon therapy or treatment. These complementary technology platforms are fully integrated with automated laboratory, biospecimen, and data management systems to facilitate detailed immune characterization of diverse patient samples at exceptional scale with uncompromising data quality and scientific rigor. These data may be linked with cutting-edge computational, bioinformatics, and machine learning pipelines to extract meaningful and actionable therapeutic

insights. The HIMCSR contributes to TCI’s mission by providing state-of-the-art technologies, project development, consistency, interpretations, and cost-effectiveness to all TCI programs.

Recent Publications

• Wilk CM, Cathomas F, Török O, Le Berichel J, Park MD, Bigenwald C, Heaton GR, Hamon P, Troncoso L, Scull BP, Dangoor D, Silvin A, Fleischmann R, Belabed M, Lin H, Merad Taouli E, Boettcher S, Li L, Aubry A, Manz MG, Kofler JK, Yue Z, Lira SA, Ginhoux F, Crary JF, McClain KL, Picarsic JL, Russo SJ, Allen CE, Merad M. Circulating senescent myeloid cells infiltrate the brain and cause neurodegeneration in histiocytic disorders. Immunity 2023; 56(12):2790-2802.e6. Read more
• Galsky MD, Daneshmand S, Izadmehr S, Gonzalez-Kozlova E, Chan KG, Lewis S, Achkar BE, Dorff TB, Cetnar JP, Neil BO, D'Souza A, Mamtani R, Kyriakopoulos C, Jun T, Gogerly-Moragoda M, Brody R, Xie H, Nie K, Kelly G, Horowitz A, Kinoshita Y, Ellis E, Nose Y, Ioannou G, Cabal R, Del Valle DM, Haines GK, Wang L, Mouw KW, Samstein RM, Mehrazin R, Bhardwaj N, Yu M, Zhao Q, Kim-Schulze S, Sebra R, Zhu J, Gnjatic S, Sfakianos J, Pal SK. Gemcitabine and cisplatin plus nivolumab as organ-sparing treatment for muscle-invasive bladder cancer: a phase 2 trial. Nat Med 2023; 29(11):2825 – 2834. Read more
• Magen A, Hamon P, Fiaschi N, Soong BY, Park MD, Mattiuz R, Humblin E, Troncoso L, D'souza D, Dawson T, Kim J, Hamel S, Buckup M, Chang C, Tabachnikova A, Schwartz H, Malissen N, Lavin Y, Soares-Schanoski A, Giotti B, Hegde S, Ioannou G, Gonzalez-Kozlova E, Hennequin C, Le Berichel J, Zhao Z, Ward SC, Fiel I, Kou B, Dobosz M, Li L, Adler C, Ni M, Wei Y, Wang W, Atwal GS, Kundu K, Cygan KJ, Tsankov AM, Rahman A, Price C, Fernandez N, He J, Gupta NT, Kim-Schulze S, Gnjatic S, Kenigsberg E, Deering RP, Schwartz M, Marron TU, Thurston G, Kamphorst AO, Merad M. Intratumoral dendritic cell-CD4+ T helper cell niches enable CD8+ T cell differentiation following PD-1 blockade in hepatocellular carcinoma. Nat Med 2023 29(6):1389-1399. Read more
• Park MD, Reyes-Torres I, LeBerichel J, Hamon P, LaMarche NM, Hegde S, Belabed M, Troncoso L, Grout JA, Magen A, Humblin E, Nair A, Molgora M, Hou J, Newman JH, Farkas AM, Leader AM, Dawson T, D'Souza D, Hamel S, Sanchez-Paulete AR, Maier B, Bhardwaj N, Martin JC, Kamphorst AO, Kenigsberg E, Casanova-Acebes M, Horowitz A, Brown BD, De Andrade LF, Colonna M, Marron TU, Merad M. TREM2 macrophages drive NK cell paucity and dysfunction in lung cancer. Nat Immunol 2023 24(5):792-801. Read more
• Martin-Serrano MA, Kepecs B, Torres-Martin M, Bramel ER, Haber PK, Merritt E, Rialdi A, Param NJ, Maeda M, Lindblad KE, Carter JK, Barcena-Varela M, Mazzaferro V, Schwartz M, Affo S, Schwabe RF, Villanueva A, Guccione E, Friedman SL, Lujambio A, Tocheva A, Llovet JM, Thung SN, Tsankov AM, Sia D. Novel microenvironment-based classification of intrahepatic cholangiocarcinoma with therapeutic implications. Gut 2023; 72(4):736 – 748. Read more

Location

1470 Madison Avenue
New York, NY 10029
Tel: 212-824-9354

Office: Hess 6 Floor, 103 Room
Labs: Hess 5 Floor, 310/313 Rooms; 6 Floor, 204/205 Rooms

Contact
Seunghee Kim-Schulze, PhD
Facility Director
seunghee.kim-schulze@mssm.edu

Directors: Ernesto Guccione, PhD and Dan Hasson, PhD

The TCI Bioinformatics for Next Generation Sequencing Shared Resource (BiNGSSR) provides next generation sequencing (NGS) focused computational analyses for cancer investigators and clinicians. The mission is to advise on experimental design and protocols related to NGS technologies, provide a broad range of bioinformatics analyses for multiple applications spanning bulk and single cell epigenomics, transcriptomics and genomics, perform data integration and visualization, and assist in cancer-focused data interpretation. BiNGSSR furthers scientific discoveries by establishing robust computational pipelines for analyzing NGS data for TCI members and offers extensive training platforms for the Mount Sinai and global research communities. BiNGSSR is also dedicated to creating opportunities to increase diversity within the STEM pipeline.

The TCI establishes Shared Resources to provide its members with coordinated access to scientific consultation, modern equipment, specialized technologies, and comprehensive institutional infrastructure to support TCI’s mission of innovative cancer research. The Associate Director of Basic Science Shared Resources unites cancer center members, TCI Senior Leadership, Shared Resources, and Mount Sinai Administration to advocate for state-of-the-art technologies and expertise that are accessible, cost-effective, evaluated, and evolving to match the needs of the cancer community. All activities related to Shared Resources management are deliberated and finalized by the TCI Shared Resources Management Team, led by Dr. Chipuk.

Please remember to acknowledge The Tisch Cancer Institute Cancer Center Support Grant (P30 CA196521) when publishing manuscripts or abstracts that utilized TCI Shared Resources.

Suggested acknowledgment language: "Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under award number P30 CA196521."

The CCSG provides TCI members with subsidized fees and priority access to many of the most utilized services within our cancer center.

Hematological Malignancies Tissue Bank

Vaccine and Cellular Therapy Laboratory

Department of Oncological Sciences Research Resources