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I completed my Bachelor of Science in Genetics and Biotechnology in 2008, and my Master¿s degree in Evolutive and Molecular Genetics in 2010 by the University of Tras-os-Montes and Alto Douro. I got my PhD fellowship in 2011 and completed my PhD in Pathology and Molecular Genetics in 2016. During that time, I received the best poster award at the IV Congress of Clinical Research in 2012 and had the chance to join the laboratory of Dr. Jorge Reis-Filho from January 2014 to July 2014 at Memorial Sloan-Kettering Cancer Center (MSKCC), New York. The molecular and single-cell work I developed in that laboratory has allowed me to be part of two main projects involving the discovery of PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary gland published in Nature Genetics in 2014, and the single-cell work applied to formalin-fixed paraffin embedded breast tissues that was published in Nature Medicine in 2017. All the research work done as a PhD student have culminated in 4 first author articles and 5 articles as a contributing author. After having completed my PhD, I re-joined the laboratory of Dr. Jorge Reis-Filho and Dr. Britta Weigelt at MSKCC as a Post-doctoral Fellow for three years (2017-2020). Their laboratory aims to bring together traditional pathological techniques with genetic analysis and functional studies to refine the classification of gynecologic cancers and to identify novel drivers and potential therapeutic targets of specific tumor types. In fact and during that time, I mainly focused on the use of high-throughput genomics to identify drivers of rare gynecologic cancer types and acquired bioinformatics skills that allowed me to accurately interpret DNA and RNA sequencing data. I presented numerous scientific posters in national and international scientific congresses and meetings, and I also presented one of my works through an oral presentation at the International Gynecologic Cancer Society in 2019, Rio de Janeiro, Brasil, regarding the genetic analysis of primary and recurrent adult granulosa cell tumors of the ovary. I also led several projects that have culminated in several scientific articles related to the clinical and biological significance of intra-tumor phenotypic and genetic heterogeneity in cancer. Still in the same laboratory, I pursued my career as a Research Associate (2020-2022) and became an expert in single-cell DNA and RNA sequencing. I recently got a six year grant from the Foundation for Science and Technology (2023-2029) as an Assistant Researcher at i3S and in the group of Cancer Signaling and Metabolism, with the aim of identifying the molecular and functional changes associated with the occurrence of familial non-medullary thyroid carcinomas and to address specific cancer risks in patients and relatives, through a complete study of a co-segregation model between rare and common genetic alterations. All the research work I have developed to date has allowed me to be an author of 94 scientific articles (several in high impact journals), of which I am first or co-first author of 22 articles, and to have an h-index of 34. Besides this, I was responsible for supervising all of the research projects conducted in the laboratory at MSKCC as well as supervising master and PhD students. I interacted with 390 collaborators in co-authoring scientific works.
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Identification

Personal identification

Full name
Arnaud Fabian da Cruz Paula

Citation names

  • Da Cruz Paula, Arnaud

Author identifiers

Ciência ID
9E10-E42E-458F
ORCID iD
0000-0001-7694-8760

Email addresses

  • arnaud.paula@i3s.up.pt (Professional)

Websites

Knowledge fields

  • Medical and Health Sciences - Basic Medicine - Pathology
  • Medical and Health Sciences - Health Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
French (Mother tongue)
English Proficiency (C2) Proficiency (C2) Advanced (C1) Proficiency (C2) Advanced (C1)
Spanish; Castilian Elementary (A2) Upper intermediate (B2) Elementary (A2) Upper intermediate (B2)
Education
Degree Classification
2016/10/31
Concluded
 Patologia e Genética Molecular (Doutoramento)
Major in Patologia e cancro
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
"Characterization of different breast cancer stem cell phenotypes in proliferative, pre-malignant and neoplastic lesions of the breast: associations with breast cancer behavior and progression" (THESIS/DISSERTATION)
 17
2008/10/01 - 2010/01/25
Concluded
 Genética Molecular Comparativa e Tecnológica (Mestrado)
Major in Patologia e Cancro
Universidade de Trás-os-Montes e Alto Douro, Portugal
"Alterações moleculares no carcinoma da mama e ovário: expressão de MCT1 e MCT4 e ampliação do HER2" (THESIS/DISSERTATION)
 16
2004/09/01 - 2008/09/01
Concluded
 Genética e Biotecnologia (Licenciatura)
Major in Genetica
Universidade de Trás-os-Montes e Alto Douro, Portugal
 14
Affiliation

Science

Category
Host institution 		Employer
2023/02/01 - Current Auxiliary Researcher (Research) Fundação para a Ciência e a Tecnologia, Portugal
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2020/11/23 - 2022/11/23 Research Assistant (Research) Memorial Sloan Kettering Cancer Center Department of Surgery, United States
2017/08/07 - 2020/11/22 Postdoc (Research) Memorial Sloan Kettering Cancer Center Department of Surgery, United States
2014/01/02 - 2014/07/31 Research Trainee (Research) Memorial Sloan Kettering Cancer Center Department of Pathology, United States
Projects

Grant

Designation Funders
2023/02/01 - 2025/02/28 Etiology resolution of familial non-medullary thyroid tumors: An orphan genetic disease
2022.05763.PTDC
Co-Principal Investigator (Co-PI)
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Associação para a Inovação e Desenvolvimento da FCT
Ongoing
2011/04/01 - 2015/04/01 Characterization of different breast cancer stem cell phenotypes in proliferative, pre-malignant and neoplastic lesions of the breast: associations with breast cancer behavior and progression
SFRH/BD/74307/2010
PhD Student Fellow
Fundação para a Ciência e a Tecnologia, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2025/02/01 - Current Decode metastatic thyroid cancer
SPEDM - 2024
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal

Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Sociedade Portuguesa de Endocrinologia Diabetes e Metabolismo
Under evaluation
2025/01/01 - Current Dissecting cellular heterogeneity in cancer: single-cell proteogenomic characterization of aggressive thyroid cancers
COMPETE2030-FEDER-00682100
Principal investigator
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Fundação para a Ciência e a Tecnologia
Under evaluation
2024/01/01 - Current The metastatic code of thyroid cancer
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Ongoing
2023/02/01 - 2029/02/01 Resolving familial non- medullary cancer aetiology: A Genetic Orphan Disease.
2022.06547.CEECIND
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Associação para a Inovação e Desenvolvimento da FCT
Ongoing
Outputs

Publications

Conference abstract
  1. Teixeira, Elisabete; Rodrigues, Lia; Cardoso, Marta; Fernandes, Cláudia; Da Cruz Paula, Arnaud; Lima, Raquel T.; Ferreira, Marta; et al. "Exploring the genetic links between voltage-gated potassium channels and familial non-medullary thyroid carcinoma: a family study". Paper presented in 46th Annual Meeting of the European Thyroid Association (ETA), 2024.
    Published
Journal article
  1. Pareja, Fresia; Dopeso, Higinio; Wang, Yi Kan; Gazzo, Andrea M.; Brown, David N.; Banerjee, Monami; Selenica, Pier; et al. "A Genomics-Driven Artificial Intelligence–Based Model Classifies Breast Invasive Lobular Carcinoma and Discovers CDH1 Inactivating Mechanisms". Cancer Research 84 20 (2024): 3478-3489. https://doi.org/10.1158/0008-5472.can-24-1322.
    10.1158/0008-5472.can-24-1322
  2. Máximo, Valdemar; Melo, Miguel; Sobrinho-Simões, Manuel; Soares, Paula; Da Cruz Paula, Arnaud. "Genomic profiling of lymph node and distant metastases from papillary and poorly differentiated thyroid carcinomas". Endocrine 86 2 (2024): 505-509. https://doi.org/10.1007/s12020-024-03968-0.
    10.1007/s12020-024-03968-0
  3. Feinberg, Jacqueline; Da Cruz Paula, Arnaud; da Silva, Edaise M.; Pareja, Fresia; Patel, Juber; Zhu, Yingjie; Selenica, Pier; et al. "Adenoid cystic carcinoma of the Bartholin's gland is underpinned by MYB- and MYBL1- rearrangements". Gynecologic Oncology 185 (2024): 58-67. https://doi.org/10.1016/j.ygyno.2024.02.015.
    10.1016/j.ygyno.2024.02.015
  4. Gordhandas, Sushmita; Da Cruz Paula, Arnaud; Kertowidjojo, Elizabeth C.; Pareja, Fresia; Dessources, Kimberly; da Silva, Edaise M.; Derakhshan, Fatemeh; et al. "Molecular profiling of primary endometrioid endometrial cancer and matched lung metastases: CTNNB1 mutation as a potential driver". Gynecologic Oncology Reports 53 (2024): 101391. https://doi.org/10.1016/j.gore.2024.101391.
    10.1016/j.gore.2024.101391
  5. Claire F. Friedman; Beryl L. Manning-Geist; Qin Zhou; Tara Soumerai; Aliya Holland; Arnaud Da Cruz Paula; Hunter Green; et al. "Nivolumab for mismatch-repair-deficient or hypermutated gynecologic cancers: a phase 2 trial with biomarker analyses". Nature Medicine (2024): https://doi.org/10.1038/s41591-024-02942-7.
    10.1038/s41591-024-02942-7
  6. Rodrigues, Lia; Da Cruz Paula, Arnaud; Soares, Paula; Vinagre, João. "Unraveling the Significance of DGCR8 and miRNAs in Thyroid Carcinoma". Cells 13 7 (2024): 561. https://doi.org/10.3390/cells13070561.
    10.3390/cells13070561
  7. Higinio Dopeso; Andrea M. Gazzo; Fatemeh Derakhshan; David N. Brown; Pier Selenica; Sahar Jalali; Arnaud Da Cruz Paula; et al. "Genomic and epigenomic basis of breast invasive lobular carcinomas lacking CDH1 genetic alterations". npj Precision Oncology (2024): https://doi.org/10.1038/s41698-024-00508-x.
    10.1038/s41698-024-00508-x
  8. Derakhshan, Fatemeh; Da Cruz Paula, Arnaud; Selenica, Pier; da Silva, Edaise M.; Grabenstetter, Anne; Jalali, Sahar; Gazzo, Andrea M.; et al. "Nonlobular Invasive Breast Carcinomas with Biallelic Pathogenic CDH1 Somatic Alterations: A Histologic, Immunophenotypic, and Genomic Characterization". Modern Pathology 37 2 (2024): 100375. https://doi.org/10.1016/j.modpat.2023.100375.
    10.1016/j.modpat.2023.100375
  9. Sia, Tiffany Y.; Yaari, Zvi; Feiner, Ron; Smith, Evan; Da Cruz Paula, Arnaud; Selenica, Pier; Doddi, Sital; et al. "Uterine washings as a novel method for early detection of ovarian cancer: Trials and tribulations". Gynecologic Oncology Reports 51 (2024): 101330. https://doi.org/10.1016/j.gore.2024.101330.
    10.1016/j.gore.2024.101330
  10. Teixeira, Elisabete; Fernandes, Cláudia; Bungardean, Maria; Paula, Arnaud Da Cruz; Lima, Raquel T.; Batista, Rui; Vinagre, João; et al. "Investigating USP42 Mutation as Underlying Cause of Familial Non-Medullary Thyroid Carcinoma". International Journal of Molecular Sciences 25 3 (2024): 1522. https://doi.org/10.3390/ijms25031522.
    10.3390/ijms25031522
  11. Zi-Ning Choo; Julie M. Behr; Aditya Deshpande; Kevin Hadi; Xiaotong Yao; Huasong Tian; Kaori Takai; et al. "Most large structural variants in cancer genomes can be detected without long reads". Nature Genetics (2023): https://doi.org/10.1038/s41588-023-01540-6.
    10.1038/s41588-023-01540-6
  12. Valdemar Máximo; Miguel Melo; Yingjie Zhu; Andrea Gazzo; Manuel Sobrinho Simões; Arnaud Da Cruz Paula; Paula Soares. "Genomic profiling of primary and metastatic thyroid cancers". Endocrine-Related Cancer (2023): https://doi.org/10.1530/ERC-23-0144.
    10.1530/ERC-23-0144
  13. Máximo, Valdemar; Melo, Miguel; Zhu, Yingjie; Gazzo, Andrea; Sobrinho Simões, Manuel; Da Cruz Paula, Arnaud; Soares, Paula. "Genomic profiling of primary and metastatic thyroid cancers". Endocrine-Related Cancer 31 2 (2023): https://doi.org/10.1530/erc-23-0144.
    10.1530/erc-23-0144
  14. Chui, M Herman; Brown, David N; Da Cruz Paula, Arnaud; da Silva, Edaise M; Momeni-Boroujeni, Amir; Reis-Filho, Jorge S; Zhang, Yanming; et al. "Decreased HER2 expression in endometrial cancer following anti-HER2 therapy". The Journal of Pathology 262 2 (2023): 129-136. https://doi.org/10.1002/path.6230.
    10.1002/path.6230
  15. Charles W. Ashley; Pier Selenica; Juber Patel; Michelle Wu; Josip Nincevic; Yulia Lakhman; Qin Zhou; et al. "High-Sensitivity Mutation Analysis of Cell-Free DNA for Disease Monitoring in Endometrial Cancer". Clinical Cancer Research (2023): https://doi.org/10.1158/1078-0432.CCR-22-1134.
    10.1158/1078-0432.CCR-22-1134
  16. Rona Yaeger; Riccardo Mezzadra; Jenna Sinopoli; Yu Bian; Michelangelo Marasco; Esther Kaplun; Yijun Gao; et al. "Molecular Characterization of Acquired Resistance to KRASG12C-EGFR Inhibition in Colorectal Cancer". Cancer Discovery (2022): https://doi.org/10.1158/2159-8290.CD-22-0405.
    10.1158/2159-8290.CD-22-0405
  17. Silveira C.; Sousa, Ana Carla; Corredeira, Patrícia; Martins, Marta; Sousa, Ana Rita; Da Cruz Paula, Arnaud; Selenica, Pier; et al. Corresponding author: Carmo-Fonseca, Maria. "Comprehensive Genomic Profiling of Cell-Free Circulating Tumor DNA Detects Response to Ribociclib Plus Letrozole in a Patient with Metastatic Breast Cancer". Biomolecules 12 12 (2022): 1818. http://dx.doi.org/10.3390/biom12121818.
    Accepted • 10.3390/biom12121818
  18. Beryl L. Manning-Geist; Ying L. Liu; Kelly A. Devereaux; Arnaud Da Cruz Paula; Qin C. Zhou; Weining Ma; Pier Selenica; et al. "Microsatellite Instability–High Endometrial Cancers with MLH1 Promoter Hypermethylation Have Distinct Molecular and Clinical Profiles". Clinical Cancer Research (2022): https://doi.org/10.1158/1078-0432.CCR-22-0713.
    10.1158/1078-0432.CCR-22-0713
  19. "Granular cell tumor of thyroid: a case series with molecular characterization highlighting unique pitfalls". Endocrine (2022): http://dx.doi.org/10.1007/s12020-022-03006-x.
    10.1007/s12020-022-03006-x
  20. Chiang, S.; Vasudevaraja, V.; Serrano, J.; Stewart, C.J.R.; Oliva, E.; Momeni-Boroujeni, A.; Jungbluth, A.A.; et al. "TSC2-mutant uterine sarcomas with JAZF1-SUZ12 fusions demonstrate hybrid features of endometrial stromal sarcoma and PEComa and are responsive to mTOR inhibition". Modern Pathology 35 1 (2022): 117-127. http://www.scopus.com/inward/record.url?eid=2-s2.0-85115683876&partnerID=MN8TOARS.
    10.1038/s41379-021-00922-7
  21. Pareja, F.; Vahdatinia, M.; Marchio, C.; Lee, S.S.K.; Da Cruz Paula, A.; Derakhshan, F.; da Silva, E.M.; et al. "Neuroendocrine tumours of the breast: A genomic comparison with mucinous breast cancers and neuroendocrine tumours of other anatomic sites". Journal of Clinical Pathology 75 1 (2022): 10-17. http://www.scopus.com/inward/record.url?eid=2-s2.0-85095957494&partnerID=MN8TOARS.
    10.1136/jclinpath-2020-207052
  22. Schwartz, C.J.; Brogi, E.; Marra, A.; Da Cruz Paula, A.F.; Nanjangud, G.J.; da Silva, E.M.; Patil, S.; et al. "The clinical behavior and genomic features of the so-called adenoid cystic carcinomas of the solid variant with basaloid features". Modern Pathology 35 2 (2022): 193-201. http://www.scopus.com/inward/record.url?eid=2-s2.0-85116356245&partnerID=MN8TOARS.
    10.1038/s41379-021-00931-6
  23. "Cancer Causative Mutations Occurring in Early Embryogenesis". Cancer Discovery (2021): candisc.1110.2021-candisc.1110.2021. http://dx.doi.org/10.1158/2159-8290.cd-21-1110.
    10.1158/2159-8290.cd-21-1110
  24. "Precision Radiotherapy: Reduction in Radiation for Oropharyngeal Cancer in the 30 ROC Trial". JNCI: Journal of the National Cancer Institute 113 6 (2021): 742-751. http://dx.doi.org/10.1093/jnci/djaa184.
    10.1093/jnci/djaa184
  25. "Clonal relationship and directionality of progression of synchronous endometrial and ovarian carcinomas in patients with DNA mismatch repair-deficiency associated syndromes". Modern Pathology 34 5 (2021): 994-1007. http://dx.doi.org/10.1038/s41379-020-00721-6.
    10.1038/s41379-020-00721-6
  26. Manning-Geist, B.L.; Gatius, S.; Liu, Y.; Gil, M.; Da Cruz Paula, A.; Tuset, N.; Abu-Rustum, N.R.; et al. "Diagnosis and management of an endometrial cancer patient with Cowden syndrome". Gynecologic Oncology 163 1 (2021): 14-21. http://www.scopus.com/inward/record.url?eid=2-s2.0-85113384193&partnerID=MN8TOARS.
    10.1016/j.ygyno.2021.08.008
  27. Moukarzel, L.A.; Ferrando, L.; Da Cruz Paula, A.; Brown, D.N.; Geyer, F.C.; Pareja, F.; Piscuoglio, S.; et al. "The genetic landscape of metaplastic breast cancers and uterine carcinosarcomas". Molecular Oncology 15 4 (2021): 1024-1039. http://www.scopus.com/inward/record.url?eid=2-s2.0-85095821581&partnerID=MN8TOARS.
    10.1002/1878-0261.12813
  28. Ashley, C.W.; Da Cruz Paula, A.; Ferrando, L.; Gularte-Mérida, R.; Sebastiao, A.P.M.; Brown, D.N.; Gazzo, A.M.; et al. "Genetic characterisation of adult primary pleomorphic uterine rhabdomyosarcoma and comparison with uterine carcinosarcoma". Histopathology 79 2 (2021): 176-186. http://www.scopus.com/inward/record.url?eid=2-s2.0-85104889414&partnerID=MN8TOARS.
    10.1111/his.14346
  29. da Silva, E.M.; Selenica, P.; Vahdatinia, M.; Pareja, F.; Da Cruz Paula, A.; Ferrando, L.; Gazzo, A.M.; et al. "TERT promoter hotspot mutations and gene amplification in metaplastic breast cancer". npj Breast Cancer 7 1 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85104557391&partnerID=MN8TOARS.
    10.1038/s41523-021-00250-8
  30. Dessources, K.; Miller, K.M.; Kertowidjojo, E.; Da Cruz Paula, A.; Zou, Y.; Selenica, P.; da Silva, E.M.; et al. "ESR1 hotspot mutations in endometrial stromal sarcoma with high-grade transformation and endocrine treatment". Modern Pathology (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85121677225&partnerID=MN8TOARS.
    10.1038/s41379-021-01003-5
  31. Bennett, J.A.; Young, R.H.; Howitt, B.E.; Croce, S.; Wanjari, P.; Zhen, C.; Da Cruz Paula, A.; et al. "A Distinctive Adnexal (Usually Paratubal) Neoplasm Often Associated with Peutz-Jeghers Syndrome and Characterized by STK11 Alterations (STK11 Adnexal Tumor): A Report of 22 Cases". American Journal of Surgical Pathology 45 8 (2021): 1061-1074. http://www.scopus.com/inward/record.url?eid=2-s2.0-85102477759&partnerID=MN8TOARS.
    10.1097/PAS.0000000000001677
  32. Huo, Y.; Selenica, P.; Mahdi, A.H.; Pareja, F.; Kyker-Snowman, K.; Chen, Y.; Kumar, R.; et al. "Genetic interactions among Brca1, Brca2, Palb2, and Trp53 in mammary tumor development". npj Breast Cancer 7 1 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85104897989&partnerID=MN8TOARS.
    10.1038/s41523-021-00253-5
  33. da Silva, E.M.; Fix, D.J.; Sebastiao, A.P.M.; Selenica, P.; Ferrando, L.; Kim, S.H.; Stylianou, A.; et al. "Mesonephric and mesonephric-like carcinomas of the female genital tract: molecular characterization including cases with mixed histology and matched metastases". Modern Pathology 34 8 (2021): 1570-1587. http://www.scopus.com/inward/record.url?eid=2-s2.0-85103350158&partnerID=MN8TOARS.
    10.1038/s41379-021-00799-6
  34. Zhao, Y.; Murciano-Goroff, Y.R.; Xue, J.Y.; Ang, A.; Lucas, J.; Mai, T.T.; Da Cruz Paula, A.F.; et al. "Diverse alterations associated with resistance to KRAS(G12C) inhibition". Nature 599 7886 (2021): 679-683. http://www.scopus.com/inward/record.url?eid=2-s2.0-85118884434&partnerID=MN8TOARS.
    10.1038/s41586-021-04065-2
  35. D'Alfonso, T.M.; Pareja, F.; Da Cruz Paula, A.; Vahdatinia, M.; Gazzo, A.; Ferrando, L.; da Silva, E.M.; et al. "Whole-exome sequencing analysis of juvenile papillomatosis and coexisting breast carcinoma". Journal of Pathology: Clinical Research 7 2 (2021): 113-120. http://www.scopus.com/inward/record.url?eid=2-s2.0-85096976532&partnerID=MN8TOARS.
    10.1002/cjp2.190
  36. Da Cruz Paula, A.; DeLair, D.F.; Ferrando, L.; Fix, D.J.; Soslow, R.A.; Park, K.J.; Chiang, S.; et al. "Genetic and molecular subtype heterogeneity in newly diagnosed early- and advanced-stage endometrial cancer". Gynecologic Oncology 161 2 (2021): 535-544. http://www.scopus.com/inward/record.url?eid=2-s2.0-85101341828&partnerID=MN8TOARS.
    10.1016/j.ygyno.2021.02.015
  37. Herman Chui, M.; Chang, J.C.; Zhang, Y.; Zehir, A.; Schram, A.M.; Konner, J.; Drilon, A.E.; et al. "Spectrum of BRAF mutations and gene rearrangements in ovarian serous carcinoma". JCO Precision Oncology 5 (2021): 1480-1492. http://www.scopus.com/inward/record.url?eid=2-s2.0-85117720583&partnerID=MN8TOARS.
    10.1200/PO.21.00055
  38. "Whole-Exome Sequencing Analysis of the Progression from Non–Low-Grade Ductal CarcinomaIn Situto Invasive Ductal Carcinoma". Clinical Cancer Research 26 14 (2020): 3682-3693. http://dx.doi.org/10.1158/1078-0432.ccr-19-2563.
    10.1158/1078-0432.ccr-19-2563
  39. Sebastiao, A.P.M.; Xu, B.; Lozada, J.R.; Pareja, F.; Geyer, F.C.; Da Cruz Paula, A.; da Silva, E.M.; et al. "Histologic spectrum of polymorphous adenocarcinoma of the salivary gland harbor genetic alterations affecting PRKD genes". Modern Pathology 33 1 (2020): 65-73. http://www.scopus.com/inward/record.url?eid=2-s2.0-85071755037&partnerID=MN8TOARS.
    10.1038/s41379-019-0351-4
  40. Olson, N.; Gularte-Mérida, R.; Selenica, P.; Da Cruz Paula, A.; Alemar, B.; Weigelt, B.; Lefferts, J.; Linos, K.. "Molecular Characterization of a Rare Dedifferentiated Liposarcoma With Rhabdomyosarcomatous Differentiation in a 24 Year Old". International Journal of Surgical Pathology 28 4 (2020): 454-463. http://www.scopus.com/inward/record.url?eid=2-s2.0-85077158209&partnerID=MN8TOARS.
    10.1177/1066896919890401
  41. Da Cruz Paula, A.; da Silva, E.M.; Segura, S.E.; Pareja, F.; Bi, R.; Selenica, P.; Kim, S.H.; et al. "Genomic profiling of primary and recurrent adult granulosa cell tumors of the ovary". Modern Pathology 33 8 (2020): 1606-1617. http://www.scopus.com/inward/record.url?eid=2-s2.0-85082135031&partnerID=MN8TOARS.
    10.1038/s41379-020-0514-3
  42. Pareja, F.; da Silva, E.M.; Frosina, D.; Geyer, F.C.; Lozada, J.R.; Basili, T.; Da Cruz Paula, A.; et al. "Immunohistochemical analysis of IDH2 R172 hotspot mutations in breast papillary neoplasms: applications in the diagnosis of tall cell carcinoma with reverse polarity". Modern Pathology 33 6 (2020): 1056-1064. http://www.scopus.com/inward/record.url?eid=2-s2.0-85077336848&partnerID=MN8TOARS.
    10.1038/s41379-019-0442-2
  43. Weis-Banke, S.E.; Lerdrup, M.; Kleine-Kohlbrecher, D.; Mohammad, F.; Sidoli, S.; Jensen, O.N.; Yanase, T.; et al. "Mutant FOXL2C134W hijacks SMAD4 and SMAD2/3 to drive adult granulosa cell tumors". Cancer Research 80 17 (2020): 3466-3479. http://www.scopus.com/inward/record.url?eid=2-s2.0-85099104308&partnerID=MN8TOARS.
    10.1158/0008-5472.CAN-20-0259
  44. Pareja, F.; Ferrando, L.; Lee, S.S.K.; Beca, F.; Selenica, P.; Brown, D.N.; Farmanbar, A.; et al. "The genomic landscape of metastatic histologic special types of invasive breast cancer". npj Breast Cancer 6 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85092599142&partnerID=MN8TOARS.
    10.1038/s41523-020-00195-4
  45. Basili, T.; Dopeso, H.; Kim, S.H.; Ferrando, L.; Pareja, F.; Da Cruz Paula, A.; da Silva, E.M.; et al. "Oncogenic properties and signaling basis of the PAX8-GLIS3 fusion gene". International Journal of Cancer 147 8 (2020): 2253-2264. http://www.scopus.com/inward/record.url?eid=2-s2.0-85085047625&partnerID=MN8TOARS.
    10.1002/ijc.33040
  46. Stasenko, M.; Tunnage, I.; Ashley, C.W.; Rubinstein, M.M.; Latham, A.J.; Da Cruz Paula, A.; Mueller, J.J.; et al. "Clinical outcomes of patients with POLE mutated endometrioid endometrial cancer". Gynecologic Oncology 156 1 (2020): 194-202. http://www.scopus.com/inward/record.url?eid=2-s2.0-85075816761&partnerID=MN8TOARS.
    10.1016/j.ygyno.2019.10.028
  47. Xu, G.; Chhangawala, S.; Cocco, E.; Razavi, P.; Cai, Y.; Otto, J.E.; Ferrando, L.; et al. "ARID1A determines luminal identity and therapeutic response in estrogen-receptor-positive breast cancer". Nature Genetics 52 2 (2020): 198-207. http://www.scopus.com/inward/record.url?eid=2-s2.0-85077862299&partnerID=MN8TOARS.
    10.1038/s41588-019-0554-0
  48. Dessources, K.; Da Cruz Paula, A.; Pareja, F.; Stylianou, A.; Cybulska, P.; Farmanbar, A.; Chandarlapaty, S.; et al. "Acquisition of APOBEC mutagenesis and microsatellite instability signatures in the development of brain metastases in low-grade, early-stage endometrioid endometrial carcinoma". JCO Precision Oncology 4 (2020): 1217-1223. http://www.scopus.com/inward/record.url?eid=2-s2.0-85095885469&partnerID=MN8TOARS.
    10.1200/PO.20.00044
  49. Zou, Y.; Turashvili, G.; Soslow, R.A.; Park, K.J.; Croce, S.; McCluggage, W.G.; Stewart, C.J.R.; et al. "High-grade transformation of low-grade endometrial stromal sarcomas lacking YWHAE and BCOR genetic abnormalities". Modern Pathology 33 9 (2020): 1861-1870. http://www.scopus.com/inward/record.url?eid=2-s2.0-85083729919&partnerID=MN8TOARS.
    10.1038/s41379-020-0535-y
  50. Conlon, N.; Da Cruz Paula, A.; Ashley, C.W.; Segura, S.; De Brot, L.; Da Silva, E.M.; Soslow, R.A.; Weigelt, B.; Delair, D.F.. "Endometrial carcinomas with a "serous" Component in young women are enriched for DNA mismatch repair deficiency, lynch syndrome, and POLE exonuclease domain mutations". American Journal of Surgical Pathology 44 5 (2020): 641-648. http://www.scopus.com/inward/record.url?eid=2-s2.0-85083543895&partnerID=MN8TOARS.
    10.1097/PAS.0000000000001461
  51. Kim, S.H.; Da Cruz Paula, A.; Basili, T.; Dopeso, H.; Bi, R.; Pareja, F.; da Silva, E.M.; et al. "Identification of recurrent FHL2-GLI2 oncogenic fusion in sclerosing stromal tumors of the ovary". Nature Communications 11 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85077465972&partnerID=MN8TOARS.
    10.1038/s41467-019-13806-x
  52. Basturk, O.; Weigelt, B.; Adsay, V.; Benhamida, J.K.; Askan, G.; Wang, L.; Arcila, M.E.; et al. "Sclerosing epithelioid mesenchymal neoplasm of the pancreas – a proposed new entity". Modern Pathology 33 3 (2020): 456-467. http://www.scopus.com/inward/record.url?eid=2-s2.0-85070297882&partnerID=MN8TOARS.
    10.1038/s41379-019-0334-5
  53. Pareja, F.; Da Cruz Paula, A.; Gularte-Mérida, R.; Vahdatinia, M.; Li, A.; Geyer, F.C.; da Silva, E.M.; et al. "Pleomorphic adenomas and mucoepidermoid carcinomas of the breast are underpinned by fusion genes". npj Breast Cancer 6 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85085998874&partnerID=MN8TOARS.
    10.1038/s41523-020-0164-0
  54. da Silva, Edaise M.; Beca, Francisco; Sebastião, Ana Paula Martins; Murray, Melissa P.; Silveira, Catarina; da Cruz Paula, Arnaud; Pareja, Fresia; et al. "Stromal MED12 exon 2 mutations in complex fibroadenomas of the breast". Journal of Clinical Pathology 75 2 (2020): 133-136. http://hdl.handle.net/10451/47536.
    10.1136/jclinpath-2020-207062
  55. "V211D Mutation in MEK1 Causes Resistance to MEK Inhibitors in Colon Cancer". Cancer Discovery 9 9 (2019): 1182-1191. http://dx.doi.org/10.1158/2159-8290.cd-19-0356.
    10.1158/2159-8290.cd-19-0356
  56. Pareja, F.; Selenica, P.; Brown, D.N.; Sebastiao, A.P.M.; da Silva, E.M.; Da Cruz Paula, A.; Del, A.; et al. "Micropapillary variant of mucinous carcinoma of the breast shows genetic alterations intermediate between those of mucinous carcinoma and micropapillary carcinoma". Histopathology 75 1 (2019): 139-145. http://www.scopus.com/inward/record.url?eid=2-s2.0-85067406114&partnerID=MN8TOARS.
    10.1111/his.13853
  57. Beca, F.; Lee, S.S.K.; Pareja, F.; Da Cruz Paula, A.; Selenica, P.; Ferrando, L.; Gularte-Mérida, R.; et al. "Whole-exome sequencing and RNA sequencing analyses of acinic cell carcinomas of the breast". Histopathology 75 6 (2019): 931-937. http://www.scopus.com/inward/record.url?eid=2-s2.0-85074009091&partnerID=MN8TOARS.
    10.1111/his.13962
  58. Marchiò, C.; Da Cruz Paula, A.; Gularte-Merida, R.; Basili, T.; Brandes, A.; da Silva, E.M.; Silveira, C.; et al. "PAX8–GLIS3 gene fusion is a pathognomonic genetic alteration of hyalinizing trabecular tumors of the thyroid". Modern Pathology 32 12 (2019): 1734-1743. http://www.scopus.com/inward/record.url?eid=2-s2.0-85068879293&partnerID=MN8TOARS.
    10.1038/s41379-019-0313-x
  59. Ashley, C.W.; Da Cruz Paula, A.; Kumar, R.; Mandelker, D.; Pei, X.; Riaz, N.; Reis-Filho, J.S.; Weigelt, B.. "Analysis of mutational signatures in primary and metastatic endometrial cancer reveals distinct patterns of DNA repair defects and shifts during tumor progression". Gynecologic Oncology 152 1 (2019): 11-19. http://www.scopus.com/inward/record.url?eid=2-s2.0-85056246361&partnerID=MN8TOARS.
    10.1016/j.ygyno.2018.10.032
  60. Pareja, F.; Da Cruz Paula, A.; Murray, M.P.; Hoang, T.; Gularte-Mérida, R.; Brown, D.; Da Silva, E.M.; et al. "Recurrent MED12 exon 2 mutations in benign breast fibroepithelial lesions in adolescents and young adults". Journal of Clinical Pathology 72 3 (2019): 258-262. http://www.scopus.com/inward/record.url?eid=2-s2.0-85057102132&partnerID=MN8TOARS.
    10.1136/jclinpath-2018-205570
  61. Pareja, F.; Geyer, F.C.; Brown, D.N.; Sebastião, A.P.M.; Gularte-Mérida, R.; Li, A.; Edelweiss, M.; et al. "Assessment of HMGA2 and PLAG1 rearrangements in breast adenomyoepitheliomas". npj Breast Cancer 5 1 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85069036429&partnerID=MN8TOARS.
    10.1038/s41523-018-0101-7
  62. Pareja, F.; Lee, J.Y.; Brown, D.N.; Piscuoglio, S.; Gularte-Mérida, R.; Selenica, P.; Da Cruz Paula, A.; et al. "The Genomic Landscape of Mucinous Breast Cancer". Journal of the National Cancer Institute 111 7 (2019): 737-741. http://www.scopus.com/inward/record.url?eid=2-s2.0-85067906127&partnerID=MN8TOARS.
    10.1093/jnci/djy216
  63. Smith, E.S.; Da Cruz Paula, A.; Cadoo, K.A.; Abu-Rustum, N.R.; Pei, X.; Brown, D.N.; Ferrando, L.; et al. "Endometrial cancers in BRCA1 or BRCA2 germline mutation carriers: Assessment of homologous recombination DNA repair defects". JCO Precision Oncology 3 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85076241358&partnerID=MN8TOARS.
    10.1200/PO.19.00103
  64. Li, Z.; Razavi, P.; Li, Q.; Toy, W.; Liu, B.; Ping, C.; Hsieh, W.; et al. "Loss of the FAT1 Tumor Suppressor Promotes Resistance to CDK4/6 Inhibitors via the Hippo Pathway". Cancer Cell 34 6 (2018): 893-905.e8. http://www.scopus.com/inward/record.url?eid=2-s2.0-85057025044&partnerID=MN8TOARS.
    10.1016/j.ccell.2018.11.006
  65. Pareja, F.; Brandes, A.H.; Basili, T.; Selenica, P.; Geyer, F.C.; Fan, D.; Da Cruz Paula, A.; et al. "Loss-of-function mutations in ATP6AP1 and ATP6AP2 in granular cell tumors". Nature Communications 9 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85052618354&partnerID=MN8TOARS.
    10.1038/s41467-018-05886-y
  66. Geyer, F.C.; Li, A.; Papanastasiou, A.D.; Smith, A.; Selenica, P.; Burke, K.A.; Edelweiss, M.; et al. "Recurrent hotspot mutations in HRAS Q61 and PI3K-AKT pathway genes as drivers of breast adenomyoepitheliomas". Nature Communications 9 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85046835936&partnerID=MN8TOARS.
    10.1038/s41467-018-04128-5
  67. Da Cruz Paula, A.; Leitão, C.; Marques, O.; Rosa, A.M.; Santos, A.H.; Rêma, A.; de Fátima Faria, M.; et al. "Molecular characterization of CD44+/CD24-/Ck+/CD45- cells in benign and malignant breast lesions". Virchows Archiv 470 3 (2017): 311-322. http://www.scopus.com/inward/record.url?eid=2-s2.0-85010782778&partnerID=MN8TOARS.
    10.1007/s00428-017-2068-4
  68. Martelotto, L.G.; Baslan, T.; Kendall, J.; Geyer, F.C.; Burke, K.A.; Spraggon, L.; Piscuoglio, S.; et al. "Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples". Nature Medicine 23 3 (2017): 376-385. http://www.scopus.com/inward/record.url?eid=2-s2.0-85011661149&partnerID=MN8TOARS.
    10.1038/nm.4279
  69. Da Cruz Paula, A.; Lopes, C.. "Implications of different cancer stem cell phenotypes in breast cancer". Anticancer Research 37 5 (2017): 2173-2183. http://www.scopus.com/inward/record.url?eid=2-s2.0-85019095594&partnerID=MN8TOARS.
    10.21873/anticanres.11552
  70. Piscuoglio, S.; Fusco, N.; Ng, C.K.Y.; Martelotto, L.G.; da Cruz Paula, A.; Katabi, N.; Rubin, B.P.; et al. "Lack of PRKD2 and PRKD3 kinase domain somatic mutations in PRKD1 wild-type classic polymorphous low-grade adenocarcinomas of the salivary gland". Histopathology 68 7 (2016): 1055-1062. http://www.scopus.com/inward/record.url?eid=2-s2.0-84952837863&partnerID=MN8TOARS.
    10.1111/his.12883
  71. Marques, O.; Porto, G.; Rêma, A.; Faria, F.; Cruz Paula, A.; Gomez-Lazaro, M.; Silva, P.; Martins da Silva, B.; Lopes, C.. "Local iron homeostasis in the breast ductal carcinoma microenvironment". BMC Cancer 16 1 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84959276692&partnerID=MN8TOARS.
    10.1186/s12885-016-2228-y
  72. Da Cruz Paula, A.; Marques, O.; Sampaio, R.; Rosa, A.; Garcia, J.; Rêma, A.; Faria, M.D.F.; et al. "Characterization of cd44+aldh1+ki-67- cells in non-malignant and neoplastic lesions of the breast". Anticancer Research 36 9 (2016): 4629-4638. http://www.scopus.com/inward/record.url?eid=2-s2.0-84991672045&partnerID=MN8TOARS.
    10.21873/anticanres.11013
  73. Guerini-Rocco, E.; Hodi, Z.; Piscuoglio, S.; Ng, C.K.Y.; Rakha, E.A.; Schultheis, A.M.; Marchiò, C.; et al. "The repertoire of somatic genetic alterations of acinic cell carcinomas of the breast: An exploratory, hypothesis-generating study". Journal of Pathology 237 2 (2015): 166-178. http://www.scopus.com/inward/record.url?eid=2-s2.0-84940891503&partnerID=MN8TOARS.
    10.1002/path.4566
  74. Da Cruz Paula, A.; Marques, O.; Rosa, A.M.; De Fátima Faria, M.; Rêma, A.; Lopes, C.. "Co-expression of stem cell markers ALDH1 and CD44 in non-malignant and neoplastic lesions of the breast". Anticancer Research 34 3 (2014): 1427-1434. http://www.scopus.com/inward/record.url?eid=2-s2.0-84899680025&partnerID=MN8TOARS.
  75. Weinreb, I.; Piscuoglio, S.; Martelotto, L.G.; Waggott, D.; Ng, C.K.Y.; Perez-Ordonez, B.; Harding, N.J.; et al. "Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands". Nature Genetics 46 11 (2014): 1166-1169. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908867220&partnerID=MN8TOARS.
    10.1038/ng.3096
Thesis / Dissertation
  1. Arnaud Fabian da Cruz Paula. "Characterization of different breast cancer stem cell phenotypes in proliferative, pre-malignant and neoplastic lesions of the breast: associations with breast cancer behavior and progression". PhD, 2016. https://hdl.handle.net/10216/86451.
  2. Paula, Arnaud Fabian da Cruz. "Alterações moleculares no carcinoma da mama e ovário: expressão de MCT1 e MCT4 e ampliação do HER2". Master, 2009. http://hdl.handle.net/10348/345.

Other

Other output
  1. Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational processes. 2021. Vázquez-García, I.; Uhlitz, F.; Ceglia, N.; Lim, J.L.P.; Wu, M.; Mohibullah, N.; Ruiz, A.E.B.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85115064475&partnerID=MN8TOARS.
    10.1101/2021.08.24.454519
  2. The impact of mutational processes on structural genomic plasticity in cancer cells. 2021. Funnell, T.; O’Flanagan, C.H.; Williams, M.J.; McPherson, A.; McKinney, S.; Kabeer, F.; Lee, H.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85110908252&partnerID=MN8TOARS.
    10.1101/2021.06.03.446999
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2019/09/20 Genetic analysis of primary and recurrent adult granulosa cell tumors of the ovary International Gynecologic cancer Society
(Rio de Janeiro, Brazil)
2012/05 Stem cell expansion in ductal carcinoma in situ of the breast. VIII National Congress of Senology
(Porto, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023/10/02 - 2027/09/30 The DGCR8 in thyroid repertoire: playing E518K classic and new opus on alterations.
Co-supervisor of Lia Rodrigues
 Biomedicina (PhD)
Universidade do Porto Faculdade de Medicina, Portugal
2024/03/01 - 2024/07/04 Clinical and genomic characterization of APOBEC-related papillary thyroid carcinomas.
Supervisor of Ricardo Campos
 Genética e Biotecnologia (Degree)
Universidade de Trás-os-Montes e Alto Douro, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2025/03/22 - 2025/03/27 Poster presentation: Co-occurrence of PI3K pathway gene alterations in endometrial cancer molecular subtypes at the single cell level.
Conference
 United States and Canadian Academy of Pathology (USCAP) Annual Meeting, Los Angeles, USA
Memorial Sloan Kettering Cancer Center, United States

Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2025/01/30 - 2025/02/02 Genomic characterization of APOBEC-related papillary thyroid carcinomas
Conference
 Congresso Português de Endocrinologia 2025
Sociedade Portuguesa de Endocrinologia Diabetes e Metabolismo, Portugal
2024/12/10 - 2024/12/14 Poster presentation: Structural Variants Affecting CDH1 in Breast Invasive Lobular Carcinoma.
Conference
 San Antonio Breast Cancer Symposium, San Antonio, USA
Memorial Sloan Kettering Cancer Center, United States

Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2024/09/07 - 2024/09/10 Poster presentation: Genomic profiling of metastases from papillary and poorly differentiated thyroid carcinomas.
Conference
 46th Annual Meeting of the European Thyroid Association (ETA)
European Thyroid Association (ETA) , Germany
2022/04/08 - 2022/04/13 Poster presentation: Single-cell DNA sequencing from frozen endometrial tumors to address clonal evolution of somatic mutations.
Congress
 American Association for Cancer Research (AACR) Annual Meeting, New Orleans, USA, 2022.
Memorial Sloan Kettering Cancer Center, United States
2020/02/28 - 2020/03/05 Poster presentation: The chronology of development of endometrioid endometrial and ovarian tumors in patients with synchronous disease.
Meeting
 United States and Canadian Academy of Pathology (USCAP) Annual Meeting, Los Angeles, USA
2020/02/28 - 2020/03/05 Poster presentation: Concordance of p53 immunohistochemistry and TP53 mutation status in endometrial cancer.
Meeting
 United States and Canadian Academy of Pathology (USCAP) Annual Meeting, Los Angeles, USA
2020/02/28 - 2020/03/05 Poster presentation: Concordance between immunohistochemistry for DNA mismatch repair proteins and next generation sequencing for the identification of microsatellite instability in endometrial cancer.
Meeting
 United States and Canadian Academy of Pathology (USCAP) Annual Meeting, Los Angeles, USA
2019/03/16 - 2019/03/21 Poster presentation: Are metaplastic breast carcinomas and uterine carcinosarcomas genetically related?
Meeting
 United States and Canadian Academy of Pathology (USCAP) Annual Meeting, Maryland, USA
2019/03/16 - 2019/03/21 Poster presentation: Are endometrial cancers arising in BRCA1/BRCA2 germline mutations carriers true BRCA1/BRCA2 cancers?
Meeting
 United States and Canadian Academy of Pathology (USCAP) Annual Meeting, Maryland, USA
2019/03/16 - 2019/03/21 Poster presentation: Uterine rhabdomyosarcomas: targeted capture and RNA sequencing analyses of three cases.
Meeting
 United States and Canadian Academy of Pathology (USCAP) Annual Meeting, Maryland, USA
2018/12/04 - 2018/12/08 Poster presentation: Metaplastic breast carcinomas and uterine carcinosarcomas are histologically and genetically related.
Congress
 San Antonio Breast Cancer Symposium, San Antonio, USA
2012 - 2012 Poster presentation: Stem cell expansion in ductal carcinoma in situ of the breast.
Congress
 European Congress of Pathology
Distinctions

Award

2012 Best poster award at the IV Congress of Clinical Research