A comprehensive molecular characterization of a claudin-low luminal B breast tumor.
Claudin‐low tumors
Luminal breast cancer
Journal
Biology direct
ISSN: 1745-6150
Titre abrégé: Biol Direct
Pays: England
ID NLM: 101258412
Informations de publication
Date de publication:
16 Aug 2024
16 Aug 2024
Historique:
received:
23
04
2024
accepted:
20
05
2024
medline:
17
8
2024
pubmed:
17
8
2024
entrez:
16
8
2024
Statut:
epublish
Résumé
Breast cancer is the most common cause of death from cancer in women. Here, we present the case of a 43-year-old woman, who received a diagnosis of claudin-low luminal B breast cancer. The lesion revealed to be a poorly differentiated high-grade infiltrating ductal carcinoma, which was strongly estrogen receptor (ER)/progesterone receptor (PR) positive and human epidermal growth factor receptor (HER2) negative. Her tumor underwent in-depth chromosomal, mutational and gene expression analyses. We found a pathogenic protein truncating mutation in the TP53 gene, which is predicted to disrupt its transcriptional activity. The patient also harbors germline mutations in some mismatch repair (MMR) genes, and her tumor displays the presence of immune infiltrates, high tumor mutational burden (TMB) status and the apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 (APOBEC3) associated signatures, which, overall, are predictive for the use of immunotherapy. Here, we propose promising prognostic indicators as well as potential therapeutic strategies based on the molecular characterization of the tumor.
Identifiants
pubmed: 39152485
doi: 10.1186/s13062-024-00482-1
pii: 10.1186/s13062-024-00482-1
doi:
Substances chimiques
Claudins
0
Types de publication
Journal Article
Case Reports
Langues
eng
Sous-ensembles de citation
IM
Pagination
66Subventions
Organisme : MUR-PNRR M4C2I1.3 PE6 project Heal Italia
ID : PE00000019
Organisme : MUR-PNRR M4C2I1.3 PE6 project Heal Italia
ID : PE00000019
Organisme : MUR-PNRR M4C2I1.3 PE6 project Heal Italia
ID : PE00000019
Organisme : MUR-PNRR M4C2I1.3 PE6 project Heal Italia
ID : PE00000019
Organisme : MUR-PNRR M4C2I1.3 PE6 project Heal Italia
ID : PE00000019
Organisme : Advanced Diagnostic- Italian network of excellence for advanced diagnosis (INNOVA)
ID : (PNC-E3-2022-23683266)
Organisme : Advanced Diagnostic- Italian network of excellence for advanced diagnosis (INNOVA)
ID : (PNC-E3-2022-23683266)
Organisme : Advanced Diagnostic- Italian network of excellence for advanced diagnosis (INNOVA)
ID : (PNC-E3-2022-23683266)
Organisme : Advanced Diagnostic- Italian network of excellence for advanced diagnosis (INNOVA)
ID : (PNC-E3-2022-23683266)
Organisme : Associazione Italiana per la Ricerca contro il Cancro
ID : 27366
Organisme : Associazione Italiana per la Ricerca contro il Cancro
ID : 22206
Organisme : Associazione Italiana per la Ricerca contro il Cancro
ID : 23232
Informations de copyright
© 2024. The Author(s).
Références
Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, et al. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61–70.
doi: 10.1038/nature11412
Yi J, Li H, Chu B, Kon N, Hu X, Hu J, et al. Inhibition of USP7 induces p53-independent tumor growth suppression in triple-negative breast cancers by destabilizing FOXM1. Cell Death Differ. 2023;30:1799–810.
pubmed: 37291217
pmcid: 10307817
doi: 10.1038/s41418-023-01180-7
Vitale I, Pietrocola F, Guilbaud E, Aaronson SA, Abrams JM, Adam D, et al. Apoptotic cell death in disease—Current understanding of the NCCD 2023. Cell Death Differ. Springer Nature; 2023. p. 1097–154.
Saatci O, Akbulut O, Cetin M, Sikirzhytski V, Uner M, Lengerli D, et al. Targeting TACC3 represents a novel vulnerability in highly aggressive breast cancers with centrosome amplification. Cell Death Differ. 2023;30:1305–19.
pubmed: 36864125
pmcid: 10154422
doi: 10.1038/s41418-023-01140-1
Li J, Dong X, Kong X, Wang Y, Li Y, Tong Y, et al. Circular RNA hsa_circ_0067842 facilitates tumor metastasis and immune escape in breast cancer through HuR/CMTM6/PD-L1 axis. Biol Direct. 2023;18.
Kuo WH, Chu PY, Wang CC, Huang PS, Chan SH. MAP7D3, a novel prognostic marker for triple-negative breast cancer, drives cell invasiveness and cancer-initiating cell properties to promote metastatic progression. Biol Direct. 2023;18.
Parker JS, Mullins M, Cheang MCU, Leung S, Voduc D, Vickery T, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol. 2023;41:4192–9.
pubmed: 37672882
doi: 10.1200/JCO.22.02511
Park S, Koo JS, Kim MS, Park HS, Lee JS, Lee JS, et al. Characteristics and outcomes according to molecular subtypes of breast cancer as classified by a panel of four biomarkers using immunohistochemistry. Breast. 2012;21:50–7.
pubmed: 21865043
doi: 10.1016/j.breast.2011.07.008
Sun G, Wei Y, Zhou B, Wang M, Luan R, Bai Y, et al. BAP18 facilitates CTCF-mediated chromatin accessible to regulate enhancer activity in breast cancer. Cell Death Differ. 2023;30:1260–78.
pubmed: 36828916
pmcid: 10154423
doi: 10.1038/s41418-023-01135-y
Zhao Y, Huang X, Zhu D, Wei M, Luo J, Yu S, et al. Deubiquitinase OTUD6A promotes breast cancer progression by increasing TopBP1 stability and rendering tumor cells resistant to DNA-damaging therapy. Cell Death Differ. 2022;29:2531–44.
pubmed: 35768646
pmcid: 9751275
doi: 10.1038/s41418-022-01036-6
Orrantia-Borunda E, Anchondo-Nuñez P, Acuña-Aguilar LE, Gómez-Valles FO, Ramírez-Valdespino CA. Subtypes of Breast Cancer. 2022.
Tran B, Bedard PL. Luminal-B breast cancer and novel therapeutic targets. Breast Cancer Res. 2011;13:221.
pubmed: 22217398
pmcid: 3326541
doi: 10.1186/bcr2904
Zhang J, Zhang G, Zhang W, Bai L, Wang L, Li T, et al. Loss of RBMS1 promotes anti-tumor immunity through enabling PD-L1 checkpoint blockade in triple-negative breast cancer. Cell Death Differ. 2022;29:2247–61.
pubmed: 35538152
pmcid: 9613699
doi: 10.1038/s41418-022-01012-0
Yin X, Teng X, Ma T, Yang T, Zhang J, Huo M, et al. RUNX2 recruits the NuRD(MTA1)/CRL4B complex to promote breast cancer progression and bone metastasis. Cell Death Differ. 2022;29:2203–17.
pubmed: 35534547
pmcid: 9613664
doi: 10.1038/s41418-022-01010-2
Loibl S, Gianni L. HER2-positive breast cancer. Lancet. 2017;389:2415–29.
pubmed: 27939064
doi: 10.1016/S0140-6736(16)32417-5
Collignon J, Lousberg L, Schroeder H, Jerusalem G. Triple-negative breast cancer: treatment challenges and solutions. Breast Cancer (Dove Med Press). 2016;8:93–107.
pubmed: 27284266
Kuo W-H, Chu P-Y, Wang C-C, Huang P-S, Chan S-H. MAP7D3, a novel prognostic marker for triple-negative breast cancer, drives cell invasiveness and cancer-initiating cell properties to promote metastatic progression. Biol Direct. 2023;18:44.
pubmed: 37550720
pmcid: 10405500
doi: 10.1186/s13062-023-00400-x
Prat A, Parker JS, Karginova O, Fan C, Livasy C, Herschkowitz JI, et al. Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res. 2010;12:R68.
pubmed: 20813035
pmcid: 3096954
doi: 10.1186/bcr2635
Yan Y, He M, Zhao L, Wu H, Zhao Y, Han L, et al. A novel HIF-2α targeted inhibitor suppresses hypoxia-induced breast cancer stemness via SOD2-mtROS-PDI/GPR78-UPRER axis. Cell Death Differ. 2022;29:1769–89.
pubmed: 35301432
pmcid: 9433403
doi: 10.1038/s41418-022-00963-8
Han X, Ren C, Lu C, Qiao P, Yang T, Yu Z. Deubiquitination of MYC by OTUB1 contributes to HK2 mediated glycolysis and breast tumorigenesis. Cell Death Differ. 2022;29:1864–73.
pubmed: 35296795
pmcid: 9433372
doi: 10.1038/s41418-022-00971-8
Prat A, Perou CM. Deconstructing the molecular portraits of breast cancer. Mol Oncol. 2011;5:5–23.
pubmed: 21147047
doi: 10.1016/j.molonc.2010.11.003
Dias K, Dvorkin-Gheva A, Hallett RM, Wu Y, Hassell J, Pond GR, et al. Claudin-low breast cancer & clinical & pathological characteristics. PLoS ONE. 2017;12: e0168669.
pubmed: 28045912
pmcid: 5207440
doi: 10.1371/journal.pone.0168669
Agostini M, Mancini M, Candi E. Long non-coding RNAs affecting cell metabolism in cancer. Biol Direct. 2022;17:26.
pubmed: 36182907
pmcid: 9526990
doi: 10.1186/s13062-022-00341-x
Fox EM, Miller TW, Balko JM, Kuba MG, Sánchez V, Smith RA, et al. A kinome-wide screen identifies the insulin/IGF-I receptor pathway as a mechanism of escape from hormone dependence in breast cancer. Cancer Res. 2011;71:6773–84.
pubmed: 21908557
pmcid: 3206206
doi: 10.1158/0008-5472.CAN-11-1295
Marra A, Trapani D, Ferraro E, Curigliano G. Mechanisms of endocrine resistance in hormone receptor-positive breast cancer. Cancer Treat Res. 2023;188:219–35.
pubmed: 38175348
doi: 10.1007/978-3-031-33602-7_9
Galea MH, Blamey RW, Elston CE, Ellis IO. The Nottingham Prognostic Index in primary breast cancer. Breast Cancer Res Treat. 1992;22:207–19.
pubmed: 1391987
doi: 10.1007/BF01840834
Pommier RM, Sanlaville A, Tonon L, Kielbassa J, Thomas E, Ferrari A, et al. Comprehensive characterization of claudin-low breast tumors reflects the impact of the cell-of-origin on cancer evolution. Nat Commun. 2020;11:3431.
pubmed: 32647202
pmcid: 7347884
doi: 10.1038/s41467-020-17249-7
Hennessy BT, Gonzalez-Angulo A-M, Stemke-Hale K, Gilcrease MZ, Krishnamurthy S, Lee J-S, et al. Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics. Cancer Res. 2009;69:4116–24.
pubmed: 19435916
pmcid: 2737191
doi: 10.1158/0008-5472.CAN-08-3441
Li J, Dong X, Kong X, Wang Y, Li Y, Tong Y, et al. Circular RNA hsa_circ_0067842 facilitates tumor metastasis and immune escape in breast cancer through HuR/CMTM6/PD-L1 axis. Biol Direct. 2023;18:48.
pubmed: 37592296
pmcid: 10436663
doi: 10.1186/s13062-023-00397-3
Massagué J. TGFbeta in cancer. Cell. 2008;134:215–30.
pubmed: 18662538
pmcid: 3512574
doi: 10.1016/j.cell.2008.07.001
Suriyamurthy S, Baker D, Ten Dijke P, Iyengar PV. Epigenetic reprogramming of TGF-β signaling in breast cancer. Cancers (Basel). 2019;11:726.
pubmed: 31137748
pmcid: 6563130
doi: 10.3390/cancers11050726
Padua D, Zhang XH-F, Wang Q, Nadal C, Gerald WL, Gomis RR, et al. TGFbeta primes breast tumors for lung metastasis seeding through angiopoietin-like 4. Cell. 2008;133:66–77.
pubmed: 18394990
pmcid: 2390892
doi: 10.1016/j.cell.2008.01.046
Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 2012;486:405–9.
pubmed: 22722202
pmcid: 4148686
doi: 10.1038/nature11154
Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013;45:1113–20.
Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med. 2004;351:2817–26.
pubmed: 15591335
doi: 10.1056/NEJMoa041588
Pant V, Sun C, Lozano G. Tissue specificity and spatio-temporal dynamics of the p53 transcriptional program. Cell Death Differ. 2023;30:897–905.
pubmed: 36755072
pmcid: 10070629
doi: 10.1038/s41418-023-01123-2
Panatta E, Butera A, Celardo I, Leist M, Melino G, Amelio I. p53 regulates expression of nuclear envelope components in cancer cells. Biol Direct. 2022;17:38.
pubmed: 36461070
pmcid: 9716746
doi: 10.1186/s13062-022-00349-3
Butera A, Roy M, Zampieri C, Mammarella E, Panatta E, Melino G, et al. p53-driven lipidome influences non-cell-autonomous lysophospholipids in pancreatic cancer. Biol Direct. 2022;17:6.
pubmed: 35255936
pmcid: 8902766
doi: 10.1186/s13062-022-00319-9
Cappello A, Tosetti G, Smirnov A, Ganini C, Yang X, Shi Y, et al. p63 orchestrates serine and one carbon metabolism enzymes expression in head and neck cancer. Biol Direct. 2023;18:73.
pubmed: 37946250
pmcid: 10636826
doi: 10.1186/s13062-023-00426-1
Tatavosian R, Donovan MG, Galbraith MD, Duc HN, Szwarc MM, Joshi MU, et al. Cell differentiation modifies the p53 transcriptional program through a combination of gene silencing and constitutive transactivation. Cell Death Differ. 2023;30:952–65.
pubmed: 36681780
pmcid: 10070495
doi: 10.1038/s41418-023-01113-4
Li J, Zhan H, Ren Y, Feng M, Wang Q, Jiao Q, et al. Sirtuin 4 activates autophagy and inhibits tumorigenesis by upregulating the p53 signaling pathway. Cell Death Differ. 2023;30:313–26.
pubmed: 36209169
doi: 10.1038/s41418-022-01063-3
Smirnov A, Cappello A, Lena AM, Anemona L, Mauriello A, Di Daniele N, et al. ZNF185 is a p53 target gene following DNA damage. Aging. 2018;10:3308–26.
pubmed: 30446632
pmcid: 6286825
doi: 10.18632/aging.101639
Slamon DJ, Leyland-Jones B, Shak S, Fuchs H, Paton V, Bajamonde A, et al. Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N Engl J Med. 2001;344:783–92.
pubmed: 11248153
doi: 10.1056/NEJM200103153441101
Curtis C, Shah SP, Chin S-F, Turashvili G, Rueda OM, Dunning MJ, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012;486:346–52.
pubmed: 22522925
pmcid: 3440846
doi: 10.1038/nature10983
Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6:pl1.
Soni UK, Jenny L, Hegde RS. IGF-1R targeting in cancer - does sub-cellular localization matter? J Exp Clin Cancer Res. 2023;42:273.
pubmed: 37858153
pmcid: 10588251
doi: 10.1186/s13046-023-02850-7
Farabaugh SM, Boone DN, Lee AV. Role of IGF1R in breast cancer subtypes, stemness, and lineage differentiation. Front Endocrinol (Lausanne). 2015;6:59.
pubmed: 25964777
doi: 10.3389/fendo.2015.00059
Jones RA, Campbell CI, Gunther EJ, Chodosh LA, Petrik JJ, Khokha R, et al. Transgenic overexpression of IGF-IR disrupts mammary ductal morphogenesis and induces tumor formation. Oncogene. 2007;26:1636–44.
pubmed: 16953219
doi: 10.1038/sj.onc.1209955
Schnarr B, Strunz K, Ohsam J, Benner A, Wacker J, Mayer D. Down-regulation of insulin-like growth factor-I receptor and insulin receptor substrate-1 expression in advanced human breast cancer. Int J Cancer. 2000;89:506–13.
pubmed: 11102895
doi: 10.1002/1097-0215(20001120)89:6<506::AID-IJC7>3.0.CO;2-F
Hernandez-Boussard T, Rodriguez-Tome P, Montesano R, Hainaut P. IARC p53 mutation database: a relational database to compile and analyze p53 mutations in human tumors and cell lines. International Agency for Research on Cancer. Hum Mutat. 1999;14:1–8.
pubmed: 10447253
doi: 10.1002/(SICI)1098-1004(1999)14:1<1::AID-HUMU1>3.0.CO;2-H
Madorsky Rowdo FP, Xiao G, Khramtsova GF, Nguyen J, Olopade OI, Martini R, et al. Patient-derived tumor organoids with p53 mutations, and not wild-type p53, are sensitive to synergistic combination PARP inhibitor treatment. bioRxiv. 2023;
Russo J, Russo IH. Molecular basis of pregnancy-induced breast cancer prevention. Horm Mol Biol Clin Investig. 2012;9:3–10.
pubmed: 25961350
doi: 10.1515/hmbci-2011-0136
Rodríguez D, Bretones G, Quesada V, Villamor N, Arango JR, López-Guillermo A, et al. Mutations in CHD2 cause defective association with active chromatin in chronic lymphocytic leukemia. Blood. 2015;126:195–202.
pubmed: 26031915
doi: 10.1182/blood-2014-10-604959
Breast Cancer Association Consortium, Dorling L, Carvalho S, Allen J, González-Neira A, Luccarini C, et al. Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women. N Engl J Med. 2021;384:428–39.
Worrillow LJ, Travis LB, Smith AG, Rollinson S, Smith AJ, Wild CP, et al. An intron splice acceptor polymorphism in hMSH2 and risk of leukemia after treatment with chemotherapeutic alkylating agents. Clin Cancer Res. 2003;9:3012–20.
pubmed: 12912950
Wang W-C, Hou T-C, Kuo C-Y, Lai Y-C. Hints from a female patient with breast cancer who later presented with Cowden syndrome. J Breast Cancer. 2020;23:430–7.
pubmed: 32908792
pmcid: 7462819
doi: 10.4048/jbc.2020.23.e25
Santos LS, Silva SN, Gil OM, Ferreira TC, Limbert E, Rueff J. Mismatch repair single nucleotide polymorphisms and thyroid cancer susceptibility. Oncol Lett. 2018;15:6715–26.
pubmed: 29616133
pmcid: 5876466
Jun S-Y, Lee E-J, Kim M-J, Chun SM, Bae YK, Hong SU, et al. Lynch syndrome-related small intestinal adenocarcinomas. Oncotarget. 2017;8:21483–500.
pubmed: 28206961
pmcid: 5400600
doi: 10.18632/oncotarget.15277
Goh JY, Feng M, Wang W, Oguz G, Yatim SMJM, Lee PL, et al. Chromosome 1q21.3 amplification is a trackable biomarker and actionable target for breast cancer recurrence. Nat Med. 2017;23:1319–30.
pubmed: 28967919
doi: 10.1038/nm.4405
Santos GC, Zielenska M, Prasad M, Squire JA. Chromosome 6p amplification and cancer progression. J Clin Pathol. 2007;60:1–7.
pubmed: 16790693
doi: 10.1136/jcp.2005.034389
Choschzick M, Lassen P, Lebeau A, Marx AH, Terracciano L, Heilenkötter U, et al. Amplification of 8q21 in breast cancer is independent of MYC and associated with poor patient outcome. Mod Pathol. 2010;23:603–10.
pubmed: 20139910
doi: 10.1038/modpathol.2010.5
Lacle MM, Kornegoor R, Moelans CB, Maes-Verschuur AH, van der Pol C, Witkamp AJ, et al. Analysis of copy number changes on chromosome 16q in male breast cancer by multiplex ligation-dependent probe amplification. Mod Pathol. 2013;26:1461–7.
pubmed: 23743929
doi: 10.1038/modpathol.2013.94
Pariyar M, Johns A, Thorne RF, Scott RJ, Avery-Kiejda KA. Copy number variation in triple negative breast cancer samples associated with lymph node metastasis. Neoplasia. 2021;23:743–53.
pubmed: 34225099
pmcid: 8259224
doi: 10.1016/j.neo.2021.05.016
Sha D, Jin Z, Budczies J, Kluck K, Stenzinger A, Sinicrope FA. Tumor mutational burden as a predictive biomarker in solid tumors. Cancer Discov. 2020;10:1808–25.
pubmed: 33139244
pmcid: 7710563
doi: 10.1158/2159-8290.CD-20-0522
Mestrallet G, Brown M, Bozkus CC, Bhardwaj N. Immune escape and resistance to immunotherapy in mismatch repair deficient tumors. Front Immunol. 2023;14:1210164.
pubmed: 37492581
pmcid: 10363668
doi: 10.3389/fimmu.2023.1210164
Sibilio P, Belardinilli F, Licursi V, Paci P, Giannini G. An integrative in-silico analysis discloses a novel molecular subset of colorectal cancer possibly eligible for immune checkpoint immunotherapy. Biol Direct. 2022;17:10.
pubmed: 35534873
pmcid: 9082922
doi: 10.1186/s13062-022-00324-y
Jakobsdottir GM, Brewer DS, Cooper C, Green C, Wedge DC. APOBEC3 mutational signatures are associated with extensive and diverse genomic instability across multiple tumour types. BMC Biol. 2022;20:117.
pubmed: 35597990
pmcid: 9124393
doi: 10.1186/s12915-022-01316-0
Periyasamy M, Singh AK, Gemma C, Kranjec C, Farzan R, Leach DA, et al. p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells. Nucleic Acids Res. 2017;45:11056–69.
pubmed: 28977491
pmcid: 5737468
doi: 10.1093/nar/gkx721
Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D, Stojanov P, et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat Genet. 2013;45:970–6.
pubmed: 23852170
pmcid: 3789062
doi: 10.1038/ng.2702
Sabelli R, Iorio E, De Martino A, Podo F, Ricci A, Viticchiè G, et al. Rhodanese-thioredoxin system and allyl sulfur compounds. FEBS J. 2008;275:3884–99.
pubmed: 18616471
doi: 10.1111/j.1742-4658.2008.06535.x
Bellomaria A, Barbato G, Melino G, Paci M, Melino S. Recognition mechanism of p63 by the E3 ligase Itch: novel strategy in the study and inhibition of this interaction. Cell Cycle. 2012;11:3638–48.
pubmed: 22935697
pmcid: 3478314
doi: 10.4161/cc.21918
Nepravishta R, Sabelli R, Iorio E, Micheli L, Paci M, Melino S. Oxidative species and S-glutathionyl conjugates in the apoptosis induction by allyl thiosulfate. FEBS J. 2012;279:154–67.
pubmed: 22035263
doi: 10.1111/j.1742-4658.2011.08407.x
Aceto A, Dragani B, Melino S, Allocati N, Masulli M, Di Ilio C, et al. Identification of an N-capping box that affects the alpha 6-helix propensity in glutathione S-transferase superfamily proteins: a role for an invariant aspartic residue. Biochem J. 1997;322(Pt 1):229–34.
pubmed: 9078266
pmcid: 1218181
doi: 10.1042/bj3220229
Fazi B, Melino S, De Rubeis S, Bagni C, Paci M, Piacentini M, et al. Acetylation of RTN-1C regulates the induction of ER stress by the inhibition of HDAC activity in neuroectodermal tumors. Oncogene. 2009;28:3814–24.
pubmed: 19668229
doi: 10.1038/onc.2009.233
Melino S, Leo S, Toska PV. Natural hydrogen sulfide donors from Allium sp. as a nutraceutical approach in Type 2 diabetes prevention and therapy. Nutrients. 2019;11:1581.
pubmed: 31336965
pmcid: 6682899
doi: 10.3390/nu11071581
Melino S, Paci M. Progress for dengue virus diseases. Towards the NS2B-NS3pro inhibition for a therapeutic-based approach. FEBS J. 2007;274:2986–3002.
pubmed: 17509079
doi: 10.1111/j.1742-4658.2007.05831.x
Scimeca M, Anemona L, Granaglia A, Bonfiglio R, Urbano N, Toschi N, et al. Plaque calcification is driven by different mechanisms of mineralization associated with specific cardiovascular risk factors. Nutr Metab Cardiovasc Dis. 2019;29:1330–6.
pubmed: 31653516
doi: 10.1016/j.numecd.2019.08.009
Scimeca M, Giocondo R, Montanaro M, Granaglia A, Bonfiglio R, Tancredi V, et al. BMP-2 variants in breast epithelial to mesenchymal transition and microcalcifications origin. Cells. 2020;9:1381.
pubmed: 32498363
pmcid: 7348762
doi: 10.3390/cells9061381
Bonfiglio R, Milano F, Cranga A, De Caro MT, Kaur Lamsira H, Trivigno D, et al. Negative prognostic value of intra-ductal fat infiltrate in breast cancer. Pathol Res Pract. 2019;215: 152634.
pubmed: 31585815
doi: 10.1016/j.prp.2019.152634
Scimeca M, Bonfiglio R, Menichini E, Albonici L, Urbano N, De Caro MT, et al. Microcalcifications drive breast cancer occurrence and development by macrophage-mediated epithelial to mesenchymal transition. Int J Mol Sci. 2019;20:5633.
pubmed: 31718020
pmcid: 6888678
doi: 10.3390/ijms20225633
Vitali A, Botta B, Delle Monache G, Zappitelli S, Ricciardi P, Melino S, et al. Purification and partial characterization of a peroxidase from plant cell cultures of Cassia didymobotrya and biotransformation studies. Biochem J. 1998;331(Pt 2):513–9.
pubmed: 9531492
pmcid: 1219383
doi: 10.1042/bj3310513
Sunzini F, De Stefano S, Chimenti MS, Melino S. hydrogen sulfide as potential regulatory gasotransmitter in arthritic diseases. Int J Mol Sci. 2020;21:1180.
pubmed: 32053981
pmcid: 7072783
doi: 10.3390/ijms21041180
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.
pubmed: 20644199
pmcid: 2928508
doi: 10.1101/gr.107524.110
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6:80–92.
pubmed: 22728672
doi: 10.4161/fly.19695
Kim S, Scheffler K, Halpern AL, Bekritsky MA, Noh E, Källberg M, et al. Strelka2: fast and accurate calling of germline and somatic variants. Nat Methods. 2018;15:591–4.
pubmed: 30013048
doi: 10.1038/s41592-018-0051-x
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009;25:2283–5.
pubmed: 19542151
pmcid: 2734323
doi: 10.1093/bioinformatics/btp373
Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics. 2012;28:311–7.
pubmed: 22155872
doi: 10.1093/bioinformatics/btr665
Ha G, Roth A, Khattra J, Ho J, Yap D, Prentice LM, et al. TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. Genome Res. 2014;24:1881–93.
pubmed: 25060187
pmcid: 4216928
doi: 10.1101/gr.180281.114
Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28:i333–9.
pubmed: 22962449
pmcid: 3436805
doi: 10.1093/bioinformatics/bts378
Manders F, Brandsma AM, de Kanter J, Verheul M, Oka R, van Roosmalen MJ, et al. MutationalPatterns: the one stop shop for the analysis of mutational processes. BMC Genom. 2022;23:134.
doi: 10.1186/s12864-022-08357-3
Bonneville R, Krook MA, Kautto EA, Miya J, Wing MR, Chen H-Z, et al. Landscape of microsatellite instability across 39 cancer types. JCO Precis Oncol. 2017;2017:1.
doi: 10.1200/PO.17.00073
Huang MN, McPherson JR, Cutcutache I, Teh BT, Tan P, Rozen SG. MSIseq: software for assessing microsatellite instability from catalogs of somatic mutations. Sci Rep. 2015;5:13321.
pubmed: 26306458
doi: 10.1038/srep13321
Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, et al. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nat Commun. 2018;9.
Becht E, Giraldo NA, Lacroix L, Buttard B, Elarouci N, Petitprez F, et al. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 2016;17.