Katherine L. Nathanson, MD

faculty photo
Pearl Basser Professor for BRCA-Related Research at the Abramson Cancer Center of the University of Pennsylvania
Department: Medicine

Contact information
421 Curie Blvd
University of Pennsylvania
Philadelphia, PA 19104
Office: 215-662-4740
B.A. (Biology)
Haverford College, Haverford, PA, 1987.
University of Pennsylvania School of Medicine, Philadelphia, PA, 1993.
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Description of Research Expertise

Hereditary Breast Cancer
The research in the Nathanson Group in hereditary breast and ovarian cancer started when I was post-doctoral fellow, training under Dr. Barbara Weber. Most recently, we have published studies demonstrating variable risks of breast and ovarian cancers with differing mutation types and locations with BRCA1 and BRCA2 (JAMA, 2015), and described the world-wide distribution of mutations (Hum Mutat, 2018). My group has evaluated the rate of moderate risk gene mutations in early onset breast cancer (Genet Med, 2015; NPJ Breast Cancer ,2017), contributed to consensus statements on the risk of these mutations (NEJM, 2015; Nat Rev Clinic Oncol, 2016), and evaluated the use of the ACMG guidelines for variant annotation of these genes (Am J Hum Genet, 2016). We published a somatic characterization of tumors associated with BRCA1/2 germline mutations and demonstrated that a significant proportion do not have allele-specific loss of heterozygosity, associated with differential genetic/genomic characteristics and survival after treatment (Nat Comm, 2017). We have preliminary data following up.

Example Projects:

1) Identification of novel breast cancer susceptibility genes using large scale sequencing in high risk and case-control cohort studies
2) Characterization of moderate penetrance breast cancer susceptibility genes in large cohorts
3) Characterization of immunogenicity in BRCA1/2 mutation associated cancers, understanding the associated molecular features and role of aneuploidy (working with cancer immunologists at Penn Medicine)
4) Understanding tumor heterogeneity in BRCA1/2 mutation associated cancers, by using single cell sequencing, high-depth targeted sequencing and large scale
5) Working with Dr. E. John Wherry’s group to elucidate immune function in healthy BRCA1/2 mutation carriers

Our research efforts in melanoma have spanned the past decade. Over this time period, we have worked with Dr. Meenhard Herlyn’s group at the Wistar Institute to lead efforts on the genetic and genomic characterization of cell lines and PDX used in pre-clinical modeling in melanoma, working, leading to over 25 publications focusing on intrinsic and acquired resistance to multiple different types of therapies. This effort cumulated in the publication of targeted massively parallel sequencing to characterize over 450 tumors, cell lines and patient derived xenografts (PDX) (Cell Reports, 2017). In the past, we also have worked on correlative studies in conjunction with clinical trials. We have two funded projects investigating inherited variation in association with outcome and immune related adverse events after treatment with checkpoint blockade, which are coming to fruition. Building upon our experience in massively parallel sequencing, the project we are doing on inherited variation in association with response to ipilimumab and our location within the Institute for Immunology, in the past two years, we also have worked on interdisciplinary projects that involve both cancer genetics and cancer immunology, specifically in melanoma (Nature, 2017; Nature Medicine, 2019), and have a funded core for massively parallel sequencing and analysis for the P01 Radiation – Immuno-oncology P01.

Example Projects:

1) Evaluating the intersection and function of non-canonical BRAF mutations with other MAPK mutations using single cell sequencing
2) Compilation of data on over 600 melanoma cell lines, PDX and tumor biopsies for in-depth analysis, with a particular view to determining if homologous recombination deficiency scores can be calculated from the targeted sequencing data (and correlate with mutation status)
3) Analysis of data on association of response and immune related adverse events after treatment with ipilimumab, focusing on specific pathways and HLA groups
4) Analysis of data on association of response and immune related adverse events after treatment with nivolumab and combination therapy (nivolumab and ipilimumab), focusing on specific pathways and HLA groups

Testicular Germ Cell Tumor
We identified the first (and only) validated candidate region associated with increased risk of TGCT in 2005 and went on to co-publish one of initial genome wide association studies (GWAS) study in TGCT (Nat Genet, 2009). GWAS in TGCT are the most successful in cancer, in terms of identifying loci with high effect sizes containing biologically plausible genes, which have implicated differences in male germ cell maturation and differentiation as being critical to disease susceptibility. We have subsequently published several other studies identifying loci associated with risk of TGCT. I currently lead the Testicular Cancer Association Consortium (TECAC), which is an international consortium of researchers (Nat Genet, 2009; Hum Mol Genet, 2011; Nat Genet, 2013; Hum Mol Genet, 2013; Hum Mol Genet, 2014; Nat Genet, 2017). These studies have furthered our understanding of the biology of TGCT as being a disease of male germ cell development, led to important genetic insights into the epidemiology of TGCT and identified the most significant loci (highest odds ratios) of any cancer GWAS. We also have generated whole exome data on several 100 patients with TGCT (JAMA Oncol, 2019), and plan more extensive sequencing, and have done ATAC-seq and Spatial-Seq (chromatin conformation capture) on multiple TGCT cell lines for post-GWA functional studies. We also heavily participated in the TCGA TGCT effort and have an ongoing collaborative project with multiple participants supported by Movember to evaluate resistance to Cisplatin in patients with TGCT.

Example Projects:

1) Identification of causal variants (SNPs) in regions associated with TGCT through in silico analysis, and subsequent functional/experimental evaluation
2) HiChIP (chromosome conformation capture using few input cells) in fetal and adult germ cells to define target-enhancer connectome and identify causal variants for TGCT
3) Whole genome sequencing of high-risk individuals with TGCT (bilateral, family history, non-white)
4) Follow-up from whole exome sequencing in case-control study to validate rare variants/genes in association with TGCT
5) Initiation and development of studies in non-whites with TGCT and women with ovarian germ tumors (also using social media)

Neuroendocrine Tumors
The Nathanson group works collaboratively with the Neuroendocrine Tumor Center at Penn Medicine on the genetics of pheochromocytoma and paraganglioma (PCC/PGL). They published their clinical genetic testing experience in PCC/PGL (Ann Surg Oncol, 2013), showing an inherited mutation rate of over 40%, accompanied by an editorial encouraging other clinicians to follow their paradigm for clinical genetic testing her group has established at Penn. Her group also was the first to identify somatic mutations in ATRX, associated with clinically aggressive disease (Nat Comm, 2015). Further, she co-led the Cancer Genome Atlas effort in PCC/PGL, which had multiple novel findings, including a recurrent fusion protein specific to this disease, and genetic/genomic predictors of poor prognosis (Cancer Cell, 2017). The group is continuing to collect samples from patients with PCC/PGL and SDHx mutations for further study.

Example Projects:

1) Evaluation of matched tumors – primary and recurrent PCC/PGL to identify mutations associated with metastatic disease
2) Evaluation of whole genome sequencing of PCC/PGL patients with no identified inherited mutations
3) Follow-up on studies suggesting that PCC/PGL with SDHx mutations have a BRCA-like phenotype, evaluating homologous recombination deficiency scores and PARP tracer up-take

Selected Publications

Dana Farengo Clark, Kara N. Maxwell, Jacquelyn Powers, David B. Lieberman, Jessica Ebrahimzadeh, Jessica M. Long, Danielle McKenna, Payal Shah, Angela Bradbury, Jennifer J.D. Morrissette, Katherine L. Nathanson, and Susan M. Domchek: Identification and Confirmation of Potentially Actionable Germline Mutations in Tumor-Only Genomic Sequencing. JCO Precision Oncology Aug 2019.

Sanchez IM, Purwin TJ, Chervoneva I, Erkes DA, Nguyen MQ, Davies MA, Nathanson KL, Kemper K, Peeper DS, Aplin AE.: In vivo ERK1/2 reporter predictively models response and resistance to combined BRAF and MEK inhibitors in melanoma. Mol Cancer Ther Jul 2019 Notes: Epub ahead of print.

Margolis DJ, Mitra N, Wubbenhorst B, D'Andrea K, Kraya AA, Hoffstad O, Shah S, Nathanson KL.: Association of Filaggrin Loss-of-Function Variants With Race in Children With Atopic Dermatitis. JAMA Dermatol Jul 2019 Notes: Epub ahead of print.

Hammet F, Mahmood K, Green TR, Nguyen-Dumont T, Southey MC, Buchanan DD, Lonie A, Nathanson KL, Couch FJ, Pope BJ, Park DJ.: Hi-Plex2: a simple and robust approach to targeted sequencing-based genetic screening. Biotechniques Jul 2019 Notes: Epub ahead of print.

Qian F, Rookus MA, Leslie G, Risch HA, Greene MH, Aalfs CM, Adank MA, Adlard J, Agnarsson BA, Ahmed M, Aittomäki K, Andrulis IL, Arnold N, Arun BK, Ausems MGEM, Azzollini J, Barrowdale D, Barwell J, Benitez J, Białkowska K, Bonadona V, Borde J, Borg A, Bradbury AR, Brunet J, Buys SS, Caldés T, Caligo MA, Campbell I, Carter J, Chiquette J, Chung WK, Claes KBM, Collée JM, Collonge-Rame MA, Couch FJ, Daly MB, Delnatte C, Diez O, Domchek SM, Dorfling CM, Eason J, Easton DF, Eeles R, Engel C, Evans DG, Faivre L, Feliubadaló L, Foretova L, Friedman E, Frost D, Ganz PA, Garber J, Garcia-Barberan V, Gehrig A, Glendon G, Godwin AK, Gómez Garcia EB, Hamann U, Hauke J, Hopper JL, Hulick PJ, Imyanitov EN, Isaacs C, Izatt L, Jakubowska A, Janavicius R, John EM, Karlan BY, Kets CM, Laitman Y, Lázaro C, Leroux D, Lester J, Lesueur F, Loud JT, Lubiński J, Łukomska A, McGuffog L, Mebirouk N, Meijers-Heijboer HEJ, Meindl A, Miller A, Montagna M, Mooij TM, Mouret-Fourme E, Nathanson KL, Nehoray B, Neuhausen SL, Nevanlinna H, Nielsen FC, Offit K, Olah E, Ong KR, Oosterwijk JC, Ottini L, Parsons MT, Peterlongo P, Pfeiler G, Pradhan N, Radice P, Ramus SJ, Rantala J, Rennert G, Robson M, Rodriguez GC, Salani R, Scheuner MT, Schmutzler RK, Shah PD, Side LE, Simard J, Singer CF, Steinemann D, Stoppa-Lyonnet D, Tan YY, Teixeira MR, Terry MB, Thomassen M, Tischkowitz M, Tognazzo S, Toland AE, Tung N, van Asperen CJ, van Engelen K, van Rensburg EJ, Venat-Bouvet L, Vierstraete J, Wagner G, Walker L, Weitzel JN, Yannoukakos D; KConFab Investigators; HEBON Investigators; GEMO Study Collaborators; EMBRACE Collaborators, Antoniou AC, Goldgar DE, Olopade OI, Chenevix-Trench G, Rebbeck TR, Huo D; CIMBA.: Mendelian randomisation study of height and body mass index as modifiers of ovarian cancer risk in 22,588 BRCA1 and BRCA2 mutation carriers. Br J Cancer Jun 2019.

Parsons MT, Tudini E, Li H, Hahnen E, Wappenschmidt B, Feliubadaló L, Aalfs CM, Agata S, Aittomäki K, Alducci E, Alonso-Cerezo MC, Arnold N, Auber B, Austin R, Azzollini J, Balmaña J, Barbieri E, Bartram CR, Blanco A, Blümcke B, Bonache S, Bonanni B, Borg Å, Bortesi B, Brunet J, Bruzzone C, Bucksch K, Cagnoli G, Caldés T, Caliebe A, Caligo MA, Calvello M, Capone GL, Caputo SM, Carnevali I, Carrasco E, Caux-Moncoutier V, Cavalli P, Cini G, Clarke EM, Concolino P, Cops EJ, Cortesi L, Couch FJ, Darder E, de la Hoya M, Dean M, Debatin I, Del Valle J, Delnatte C, Derive N, Diez O, Ditsch N, Domchek SM, Dutrannoy V, Eccles DM, Ehrencrona H, Enders U, Evans DG, Faust U, Felbor U, Feroce I, Fine M, Galvao HCR, Gambino G, Gehrig A, Gensini F, Gerdes AM, Germani A, Giesecke J, Gismondi V, Gómez C, Gómez Garcia EB, González S, Grau E, Grill S, Gross E, Guerrieri-Gonzaga A, Guillaud-Bataille M, Gutiérrez-Enríquez S, Haaf T, Hackmann K, Hansen TVO, Harris M, Hauke J, Heinrich T, Hellebrand H, Herold KN, Honisch E, Horvath J, Houdayer C, Hübbel V, Iglesias S, Izquierdo A, James PA, Janssen LAM, Jeschke U, Kaulfuß S, Keupp K, Kiechle M, Kölbl A, Krieger S, Kruse TA, Kvist A, Lalloo F, Larsen M, Lattimore VL, Lautrup C, Ledig S, Leinert E, Lewis AL, Lim J, Loeffler M, López-Fernández A, Lucci-Cordisco E, Maass N, Manoukian S, Marabelli M, Matricardi L, Meindl A, Michelli RD, Moghadasi S, Moles-Fernández A, Montagna M, Montalban G, Monteiro AN, Montes E, Mori L, Moserle L, Müller CR, Mundhenke C, Naldi N, Nathanson KL, Navarro M, Nevanlinna H, Nichols CB, Niederacher D, Nielsen HR, Ong KR, Pachter N, Palmero EI, Papi L, Pedersen IS, Peissel B, Pérez-Segura P, Pfeifer K, Pineda M, Pohl-Rescigno E, Poplawski NK, Porfirio B, Quante AS, Ramser J, Reis RM, Revillion F, Rhiem K, Riboli B, Ritter J, Rivera D, Rofes P, Rump A, Salinas M, Sánchez de Abajo AM, Schmidt G, Schoenwiese U, Seggewiß J, Solanes A, Steinemann D, Stiller M, Stoppa-Lyonnet D, Sullivan KJ, Susman R, Sutter C, Tavtigian SV, Teo SH, Teulé A, Thomassen M, Tibiletti MG, Tognazzo S, Toland AE, Tornero E, Törngren T, Torres-Esquius S, Toss A, Trainer AH, van Asperen CJ, van Mackelenbergh MT, Varesco L, Vargas-Parra G, Varon R, Vega A, Velasco Á, Vesper AS, Viel A, Vreeswijk MPG, Wagner SA, Waha A, Walker LC, Walters RJ, Wang-Gohrke S, Weber BHF, Weichert W, Wieland K, Wiesmüller L, Witzel I, Wöckel A, Woodward ER, Zachariae S, Zampiga V, Zeder-Göß C; KConFab Investigators, Lázaro C, De Nicolo A, Radice P, Engel C, Schmutzler RK, Goldgar DE, Spurdle AB: Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification. Hum Mutat May 2019 Notes: Epub ahead of print.

Friebel TM, Andrulis IL, Balmaña J, Blanco AM, Couch FJ, Daly MB, Domchek SM, Easton DF, Foulkes WD, Ganz PA, Garber J, Glendon G, Greene MH, Hulick PJ, Isaacs C, Jankowitz RC, Karlan BY, Kirk J, Kwong A, Lee A, Lesueur F, Lu KH, Nathanson KL, Neuhausen SL, Offit K, Palmero EI, Sharma P, Tischkowitz M, Toland AE, Tung N, van Rensburg EJ, Vega A, Weitzel JN; GEMO Study Collaborators, Hoskins KF, Maga T, Parsons MT, McGuffog L, Antoniou AC, Chenevix-Trench G, Huo D, Olopade OI, Rebbeck TR: BRCA1 and BRCA2 Pathogenic Sequence Variants in Women of African Origin or Ancestry. Hum Mutat May 2019 Notes: Epub ahead of print.

Ferreira MA, Gamazon ER, Al-Ejeh F, Aittomäki K, Andrulis IL, Anton-Culver H, Arason A, Arndt V, Aronson KJ, Arun BK, Asseryanis E, Azzollini J, Balmaña J, Barnes DR, Barrowdale D, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Białkowska K, Blomqvist C, Bogdanova NV, Bojesen SE, Bolla MK, Borg A, Brauch H, Brenner H, Broeks A, Burwinkel B, Caldés T, Caligo MA, Campa D, Campbell I, Canzian F, Carter J, Carter BD, Castelao JE, Chang-Claude J, Chanock SJ, Christiansen H, Chung WK, Claes KBM, Clarke CL; EMBRACE Collaborators; GC-HBOC Study Collaborators; GEMO Study Collaborators, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, de la Hoya M, Dennis J, Devilee P, Diez O, Dörk T, Dunning AM, Dwek M, Eccles DM, Ejlertsen B, Ellberg C, Engel C, Eriksson M, Fasching PA, Fletcher O, Flyger H, Friedman E, Frost D, Gabrielson M, Gago-Dominguez M, Ganz PA, Gapstur SM, Garber J, García-Closas M, García-Sáenz JA, Gaudet MM, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Greene MH, Gronwald J, Guénel P, Haiman CA, Hall P, Hamann U, He W, Heyworth J, Hogervorst FBL, Hollestelle A, Hoover RN, Hopper JL, Hulick PJ, Humphreys K, Imyanitov EN; ABCTB Investigators; HEBON Investigators; BCFR Investigators, Isaacs C, Jakimovska M, Jakubowska A, James PA, Janavicius R, Jankowitz RC, John EM, Johnson N, Joseph V, Karlan BY, Khusnutdinova E, Kiiski JI, Ko YD, Jones ME, Konstantopoulou I, Kristensen VN, Laitman Y, Lambrechts D, Lazaro C, Leslie G, Lester J, Lesueur F, Lindström S, Long J, Loud JT, Lubiński J, Makalic E, Mannermaa A, Manoochehri M, Margolin S, Maurer T, Mavroudis D, McGuffog L, Meindl A, Menon U, Michailidou K, Miller A, Montagna M, Moreno F, Moserle L, Mulligan AM, Nathanson KL, Neuhausen SL, Nevanlinna H, Nevelsteen I, Nielsen FC, Nikitina-Zake L, Nussbaum RL, Offit K, Olah E, Olopade OI, Olsson H, Osorio A, Papp J, Park-Simon TW, Parsons MT, Pedersen IS, Peixoto A, Peterlongo P, Pharoah PDP, Plaseska-Karanfilska D, Poppe B, Presneau N, Radice P, Rantala J, Rennert G, Risch HA, Saloustros E, Sanden K, Sawyer EJ, Schmidt MK, Schmutzler RK, Sharma P, Shu XO, Simard J, Singer CF, Soucy P, Southey MC, Spinelli JJ, Spurdle AB, Stone J, Swerdlow AJ, Tapper WJ, Taylor JA, Teixeira MR, Terry MB, Teulé A, Thomassen M, Thöne K, Thull DL, Tischkowitz M, Toland AE, Torres D, Truong T, Tung N, Vachon CM, van Asperen CJ, van den Ouweland AMW, van Rensburg EJ, Vega A, Viel A, Wang Q, Wappenschmidt B, Weitzel JN, Wendt C, Winqvist R, Yang XR, Yannoukakos D, Ziogas A, Kraft P, Antoniou AC, Zheng W, Easton DF, Milne RL, Beesley J, Chenevix-Trench G.: Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer. Nat Commun 10(1): 1741, Apr 2019.

Kraya AA, Maxwell KN, Wubbenhorst B, Wenz BM, Pluta J, Rech AJ, Dorfman LM, Lunceford N, Barrett A, Mitra N, Morrissette JJ, Feldman M, Nayak A, Domchek SM, Vonderheide RH, Nathanson KL: Genomic signatures predict the immunogenicity of BRCA-deficient breast cancer. Clin Cancer Res Mar 2019 Notes: Epub ahead of print.

Huang AC, Orlowski RJ, Xu X, Mick R, George SM, Yan PK, Manne S, Kraya AA, Wubbenhorst B, Dorfman L, D'Andrea K, Wenz BM, Liu S, Chilukuri L, Kozlov A, Carberry M, Giles L, Kier MW, Quagliarello F, McGettigan S, Kreider K, Annamalai L, Zhao Q, Mogg R, Xu W, Blumenschein WM, Yearley JH, Linette GP, Amaravadi RK, Schuchter LM, Herati RS, Bengsch B, Nathanson KL, Farwell MD, Karakousis GC, Wherry EJ, Mitchell TC: A single dose of neoadjuvant PD-1 blockade predicts clinical outcomes in resectable melanoma. Nat Med 25(3): 454-461, Mar 2019.

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Last updated: 09/20/2019
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