MLH1 intronic variants mapping to+5 position of splice donor sites lead to deleterious effects on RNA splicing

Author(s):Show less -

Pinero, Tamara Alejandra ^{[1, 2]} ; Soukarieh, Omar ^[3] ; Rolain, Marion ^[3] ; Alvarez, Karin ^[4] ; Lopez-Kostner, Francisco ^[4] ; Torrezan, Giovana Tardin ^[5] ; Carraro, Dirce Maria ^[5] ; De Oliveira Nascimento, Ivana Lucia ^[6] ; Bomfim, Thais Ferreira ^[6] ; Machado-Lopes, Taisa Manuela Bonfim ^[6] ; Freitas, Juliana Cortes ^{[6, 7]} ; Toralles, Maria Betania ^[6] ; Sandes, Kiyoko Abe ^[6] ; Rossi, Benedito Mauro ^[8] ; Junior, Samuel Aguiar ^[9] ; Meira, Joanna ^[10] ; Dominguez-Valentin, Mev ^{[11, 12]} ; Moller, Pal ^[13] ; Vaccaro, Carlos Alberto ^{[1, 2]} ; Martins, Alexandra ^[3] ; Pavicic, Walter Hernan ^{[1, 2]}

Affiliation:Show less -

^[1] Consejo Nacl Invest Cient & Tecn, IUHI, HIBA, Inst Med Traslac & Ingn Biomed IMTIB, C1199ABH, Buenos Aires, DF - Argentina

^[2] Hosp Italiano Buenos Aires, Programa Canc Hereditario ProCanHe, C1199ABH, Buenos Aires, DF - Argentina

^[3] Normandie Univ, UNIROUEN, Normandy Ctr Genom & Personalized Med, INSERM, IRIB, U1245, Rouen 76183 1 - France

^[4] Clin Las Condes, Unidad Coloproctol, Lab Oncol & Genet Mol, Santiago 7591046 - Chile

^[5] AC Camargo Canc Ctr, Genom & Mol Biol Grp, Int Res Ctr, Sao Paulo 01508010 - Brazil

^[6] Univ Fed Bahia, Inst Ciencias Saude, Lab Imunol & Biol Mol, Salvador 40110902, BA - Brazil

^[7] Univ Estado Bahia, Dept Ciencias Vida, Salvador 41150000, BA - Brazil

^[8] Hosp Sirio Libanes, Sao Paulo 01308050 - Brazil

^[9] AC Camargo Canc Ctr, Pelv Surg Dept, Colorectal Tumor Nucleus, Sao Paulo 01509010, SP - Brazil

^[10] Univ Fed Bahia, Hosp Univ Prof Edgard Santos, Salvador 40301155, BA - Brazil

^[11] Oslo Univ Hosp, Inst Canc Res, Dept Tumor Biol, Oslo 0369 - Norway

^[12] Univ Catolica Trujillo, Inst Invest, Chimbote - Peru

^[13] Oslo Univ Hosp, Dept Tumor Biol, Norwegian Radium Hosp, Oslo 0369 - Norway

• Document type: Journal article
• Source: FAMILIAL CANCER; v. 19, n. 4 MAY 2020.
• Web of Science Citations: 1

Abstract

Germline pathogenic variants in the DNA mismatch repair genes (MMR): MLH1, MSH2, MSH6, and PMS2, are causative of Lynch syndrome (LS). However, many of the variants mapping outside the invariant splice site positions (IVS +/- 1, IVS +/- 2) are classified as variants of unknown significance (VUS). Three such variants (MLH1 c.588+5G>C, c.588+5G>T and c.677+5G>A) were identified in 8 unrelated LS families from Argentina, Brazil and Chile. Herein, we collected clinical information on these families and performed segregation analysis and RNA splicing studies to assess the implication of these VUS in LS etiology. Pedigrees showed a clear pattern of variant co-segregation with colorectal cancer and/or other LS-associated malignancies. Tumors presented deficient expression of MLH1-PMS2 proteins in 7/7 of the LS families, and MSI-high status in 3/3 cases. Moreover, RNA analyses revealed that c.588+5G>C and c.588+5G>T induce skipping of exon 7 whereas c.677+5G>A causes skipping of exon 8. In sum, we report that the combined clinical findings in the families and the molecular studies provided the evidences needed to demonstrate that the three MLH1 variants are causative of LS and to classify c.588+5G>C and c.677+5G>A as class 5 (pathogenic), and c.588+5G>T as class 4 (likely-pathogenic). Our findings underline the importance of performing clinical and family analyses, as well as RNA splicing assays in order to determine the clinical significance of intronic variants, and contribute to the genetic counseling and clinical management of patients and their relatives. (AU)

• FAPESP's process: 14/50943-1 - INCT 2014: on Oncogenomics and Therapeutic Inovations
• Grantee: Dirce Maria Carraro
• Support Opportunities: Research Projects - Thematic Grants