Transcriptome Analysis of Diffuse Large B-Cell Lymphoma Cells Inducibly Expressing MyD88 L265P Mutation Identifies Upregulated CD44, LGALS3, NFKBIZ, and BATF as Downstream Targets of Oncogenic NF-κB Signaling
Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
ID:90140
Ministry of Education, Youth and Sports of the Czech Republic e-INFRA CZ
CZ-DRO-FNOs/2022
Ministry of Health, Czech Republic - conceptual development of research organization (FNOs/2022)
GA CR 18-24070Y
Czech Science Foundation
N.A.
Podpora vědy a výzkumu v Moravskoslezském kraji 2021
CZ.02.2.69/0.0/0.0/19_073/0016939
Interní grantová soutěž pro studenty doktorského studia na Ostravské univerzitě
N.A.
Leukemia & Lymphoma Society
N.A.
American Society of Hematology
27750
Italian Association for Cancer Research
CZ.02.1.01/0.0/0.0/17_049/0008440
European Regional Development Fund
PubMed
36982699
PubMed Central
PMC10057398
DOI
10.3390/ijms24065623
PII: ijms24065623
Knihovny.cz E-zdroje
- Klíčová slova
- CD44, DLBCL, Galectin-3, LGALS3, MYD88, NF-kB, lymphoma, oncogenic signaling,
- MeSH
- adaptorové proteiny signální transdukční metabolismus MeSH
- antigeny CD44 genetika metabolismus MeSH
- difúzní velkobuněčný B-lymfom * patologie MeSH
- galektin 3 metabolismus MeSH
- lidé MeSH
- mutace MeSH
- NF-kappa B * genetika metabolismus MeSH
- protein MyD88 genetika metabolismus MeSH
- stanovení celkové genové exprese MeSH
- transkripční faktory bZIP genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- adaptorové proteiny signální transdukční MeSH
- antigeny CD44 MeSH
- BATF protein, human MeSH Prohlížeč
- CD44 protein, human MeSH Prohlížeč
- galektin 3 MeSH
- NF-kappa B * MeSH
- NFKBIZ protein, human MeSH Prohlížeč
- protein MyD88 MeSH
- transkripční faktory bZIP MeSH
During innate immune responses, myeloid differentiation primary response 88 (MyD88) functions as a critical signaling adaptor protein integrating stimuli from toll-like receptors (TLR) and the interleukin-1 receptor (IL-1R) family and translates them into specific cellular outcomes. In B cells, somatic mutations in MyD88 trigger oncogenic NF-κB signaling independent of receptor stimulation, which leads to the development of B-cell malignancies. However, the exact molecular mechanisms and downstream signaling targets remain unresolved. We established an inducible system to introduce MyD88 to lymphoma cell lines and performed transcriptomic analysis (RNA-seq) to identify genes differentially expressed by MyD88 bearing the L265P oncogenic mutation. We show that MyD88L265P activates NF-κB signaling and upregulates genes that might contribute to lymphomagenesis, including CD44, LGALS3 (coding Galectin-3), NFKBIZ (coding IkBƺ), and BATF. Moreover, we demonstrate that CD44 can serve as a marker of the activated B-cell (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) and that CD44 expression is correlated with overall survival in DLBCL patients. Our results shed new light on the downstream outcomes of MyD88L265P oncogenic signaling that might be involved in cellular transformation and provide novel therapeutical targets.
Candiolo Cancer Institute FPO IRCCS 10060 Candiolo Italy
Department of Haematooncology Faculty of Medicine University of Ostrava 70300 Ostrava Czech Republic
Department of Haematooncology University Hospital Ostrava 70800 Ostrava Czech Republic
Faculty of Science University of Ostrava 70100 Ostrava Czech Republic
Zobrazit více v PubMed
Deguine J., Barton G.M. MyD88: A central player in innate immune signaling. F1000Prime Rep. 2014;6:97. doi: 10.12703/P6-97. PubMed DOI PMC
Gay N.J., Symmons M.F., Gangloff M., Bryant C.E. Assembly and localization of Toll-like receptor signalling complexes. Nat. Rev. Immunol. 2014;14:546–558. doi: 10.1038/nri3713. PubMed DOI
Motshwene P.G., Moncrieffe M.C., Grossmann J.G., Kao C., Ayaluru M., Sandercock A.M., Robinson C.V., Latz E., Gay N.J. An Oligomeric Signaling Platform Formed by the Toll-like Receptor Signal Transducers MyD88 and IRAK-4. J. Biol. Chem. 2009;284:25404–25411. doi: 10.1074/jbc.M109.022392. PubMed DOI PMC
Ngo V.N., Young R.M., Schmitz R., Jhavar S., Xiao W., Lim K.-H., Kohlhammer H., Xu W., Yang Y., Zhao H., et al. Oncogenically active MYD88 mutations in human lymphoma. Nature. 2011;470:115–119. doi: 10.1038/nature09671. PubMed DOI PMC
Takeda K., Akira S. TLR signaling pathways. Semin. Immunol. 2004;16:3–9. doi: 10.1016/j.smim.2003.10.003. PubMed DOI
Picard C., Casanova J.L., Puel A. Infectious Diseases in Patients with IRAK-4, MyD88, NEMO, or IκBα Deficiency. Clin. Microbiol. Rev. 2011;24:490–497. doi: 10.1128/CMR.00001-11. PubMed DOI PMC
Yun S., Johnson A.C., Okolo O.N., Arnold S.J., McBride A., Zhang L., Baz R.C., Anwer F. Waldenström Macroglobulinemia: Review of Pathogenesis and Management. Clin. Lymphoma Myeloma Leuk. 2017;17:252–262. doi: 10.1016/j.clml.2017.02.028. PubMed DOI PMC
Yang G., Wang J., Tan L., Munshi M., Liu X., Kofides A., Chen J.G., Tsakmaklis N., Demos M.G., Guerrera M.L., et al. The HCK/BTK inhibitor KIN-8194 is active in MYD88-driven lymphomas and overcomes mutated BTKCys481 ibrutinib resistance. Blood. 2021;138:1966–1979. doi: 10.1182/blood.2021011405. PubMed DOI PMC
Cohen P., Kelsall I.R., Nanda S.K., Zhang J. HOIL-1, an atypical E3 ligase that controls MyD88 signalling by forming ester bonds between ubiquitin and components of the Myddosome. Adv. Biol. Regul. 2020;75:100666. doi: 10.1016/j.jbior.2019.100666. PubMed DOI PMC
Yang Y., Schmitz R., Mitala J., Whiting A., Xiao W., Ceribelli M., Wright G.W., Zhao H., Yang Y., Xu W., et al. Essential Role of the Linear Ubiquitin Chain Assembly Complex in Lymphoma Revealed by Rare Germline Polymorphisms. Cancer Discov. 2014;4:480–493. doi: 10.1158/2159-8290.CD-13-0915. PubMed DOI PMC
Dobashi A. Molecular Pathogenesis of Diffuse Large B-Cell Lymphoma. J. Clin. Exp. Hematop. 2016;56:71–78. doi: 10.3960/jslrt.56.71. PubMed DOI PMC
Krappmann D., Vincendeau M. Mechanisms of NF-κB deregulation in lymphoid malignancies. Semin. Cancer Biol. 2016;39:3–14. doi: 10.1016/j.semcancer.2016.05.002. PubMed DOI
Yu X., Li W., Deng Q., Li L., Hsi E.D., Young K.H., Zhang M., Li Y. MYD88 L265P Mutation in Lymphoid Malignancies. Cancer Res. 2018;78:2457–2462. doi: 10.1158/0008-5472.CAN-18-0215. PubMed DOI
Wang J.Q., Jeelall Y.S., Ferguson L.L., Horikawa K. Toll-Like Receptors and Cancer: MYD88 Mutation and Inflammation. Front. Immunol. 2014;5:367. doi: 10.3389/fimmu.2014.00367. PubMed DOI PMC
Weber A.N.R., Gloria Y.C., Çınar Ö., Reinhardt H.C., Pezzutto A., Wolz O.O. Oncogenic MYD88 mutations in lymphoma: Novel insights and therapeutic possibilities. Cancer Immunol. Immunother. 2018;67:1797–1807. doi: 10.1007/s00262-018-2242-9. PubMed DOI PMC
Treon S.P., Xu L., Yang G., Zhou Y., Liu X., Cao Y., Sheehy P., Manning R.J., Patterson C.J., Tripsas C., et al. MYD88 L265P Somatic Mutation in Waldenström’s Macroglobulinemia. N. Engl. J. Med. 2012;367:826–833. doi: 10.1056/NEJMoa1200710. PubMed DOI
Varettoni M., Arcaini L., Zibellini S., Boveri E., Rattotti S., Riboni R., Corso A., Orlandi E., Bonfichi M., Gotti M., et al. Prevalence and clinical significance of the MYD88 (L265P) somatic mutation in Waldenström’s macroglobulinemia and related lymphoid neoplasms. Blood. 2013;121:2522–2528. doi: 10.1182/blood-2012-09-457101. PubMed DOI
de Groen R.A.L., Schrader A.M.R., Kersten M.J., Pals S.T., Vermaat J.S.P. MYD88 in the driver’s seat of B-cell lymphomagenesis: From molecular mechanisms to clinical implications. Haematologica. 2019;104:2337–2348. doi: 10.3324/haematol.2019.227272. PubMed DOI PMC
Loiarro M., Volpe E., Ruggiero V., Gallo G., Furlan R., Maiorino C., Battistini L., Sette C. Mutational Analysis Identifies Residues Crucial for Homodimerization of Myeloid Differentiation Factor 88 (MyD88) and for Its Function in Immune Cells. J. Biol. Chem. 2013;288:30210–30222. doi: 10.1074/jbc.M113.490946. PubMed DOI PMC
Avbelj M., Wolz O.O., Fekonja O., Benčina M., Repič M., Mavri J., Krüger J., Schärfe C., Garcia M.D., Panter G., et al. Activation of lymphoma-associated MyD88 mutations via allostery-induced TIR-domain oligomerization. Blood. 2014;124:3896. doi: 10.1182/blood-2014-05-573188. PubMed DOI PMC
Wang J.Q., Jeelall Y.S., Beutler B., Horikawa K., Goodnow C.C. Consequences of the recurrent MYD88L265P somatic mutation for B cell tolerance. J. Exp. Med. 2014;211:413–426. doi: 10.1084/jem.20131424. PubMed DOI PMC
Knittel G., Liedgens P., Korovkina D., Seeger J.M., Al-Baldawi Y., Al-Maarri M., Fritz C., Vlantis K., Bezhanova S., Scheel A.H., et al. B-cell–specific conditional expression of Myd88p.L252P leads to the development of diffuse large B-cell lymphoma in mice. Blood. 2016;127:2732–2741. doi: 10.1182/blood-2015-11-684183. PubMed DOI PMC
Sewastianik T., Guerrera M.L., Adler K., Dennis P.S., Wright K., Shanmugam V., Huang Y., Tanton H., Jiang M., Kofides A., et al. Human MYD88L265P is insufficient by itself to drive neoplastic transformation in mature mouse B cells. Blood Adv. 2019;3:3360–3374. doi: 10.1182/bloodadvances.2019000588. PubMed DOI PMC
Rodriguez S., Celay J., Goicoechea I., Jimenez C., Botta C., Garcia-Barchino M.J., Garces J.J., Larrayoz M., Santos S., Alignani D., et al. Preneoplastic somatic mutations including MYD88 L265P in lymphoplasmacytic lymphoma. Sci. Adv. 2022;8 doi: 10.1126/sciadv.abl4644. PubMed DOI PMC
Flümann R., Rehkämper T., Nieper P., Pfeiffer P., Holzem A., Klein S., Bhatia S., Kochanek M., Kisis I., Pelzer B.W., et al. An Autochthonous Mouse Model of Myd88- and BCL2-Driven Diffuse Large B-cell Lymphoma Reveals Actionable Molecular Vulnerabilities. Blood Cancer Discov. 2021;2:70–91. doi: 10.1158/2643-3230.BCD-19-0059. PubMed DOI PMC
Phelan J.D., Young R.M., Webster D.E., Roulland S., Wright G.W., Kasbekar M., Shaffer A.L., Ceribelli M., Wang J.Q., Schmitz R., et al. A multiprotein supercomplex controlling oncogenic signalling in lymphoma. Nature. 2018;560:387–391. doi: 10.1038/s41586-018-0290-0. PubMed DOI PMC
Yang G., Zhou Y., Liu X., Xu L., Cao Y., Manning R.J., Patterson C.J., Buhrlage S.J., Gray N., Tai Y.T., et al. A mutation in MYD88 (L265P) supports the survival of lymphoplasmacytic cells by activation of Bruton tyrosine kinase in Waldenström macroglobulinemia. Blood. 2013;122:1222–1232. doi: 10.1182/blood-2012-12-475111. PubMed DOI
An B., Zhu S., Li T., Wu J., Zang G., Lv X., Qiao Y., Huang J., Shao Y., Cui J., et al. A Dual TLR7/TLR9 Inhibitor HJ901 Inhibits ABC-DLBCL Expressing the MyD88 L265P Mutation. Front. Cell Dev. Biol. 2020;8:262. doi: 10.3389/fcell.2020.00262. PubMed DOI PMC
Dubois S., Viailly P.J., Bohers E., Bertrand P., Ruminy P., Marchand V., Maingonnat C., Mareschal S., Picquenot J.M., Penther D., et al. Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and non-L265P–Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases. Clin. Cancer Res. 2017;23:2232–2244. doi: 10.1158/1078-0432.CCR-16-1922. PubMed DOI
Radke J., Ishaque N., Koll R., Gu Z., Schumann E., Sieverling L., Uhrig S., Hübschmann D., Toprak U.H., López C., et al. The genomic and transcriptional landscape of primary central nervous system lymphoma. Nat. Commun. 2022;13:2558. doi: 10.1038/s41467-022-30050-y. PubMed DOI PMC
Schmitz R., Wright G.W., Huang D.W., Johnson C.A., Phelan J.D., Wang J.Q., Roulland S., Kasbekar M., Young R.M., Shaffer A.L., et al. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N. Engl. J. Med. 2018;378:1396–1407. doi: 10.1056/NEJMoa1801445. PubMed DOI PMC
Tarantelli C., Gaudio E., Arribas A.J., Kwee I., Hillmann P., Rinaldi A., Cascione L., Spriano F., Bernasconi E., Guidetti F., et al. PQR309 Is a Novel Dual PI3K/mTOR Inhibitor with Preclinical Antitumor Activity in Lymphomas as a Single Agent and in Combination Therapy. Clin. Cancer Res. 2018;24:120–129. doi: 10.1158/1078-0432.CCR-17-1041. PubMed DOI
Alcoceba M., García-Álvarez M., Medina A., Maldonado R., González-Calle V., Chillón M.C., Sarasquete M.E., González M., García-Sanz R., Jiménez C. MYD88 Mutations: Transforming the Landscape of IgM Monoclonal Gammopathies. Int. J. Mol. Sci. 2022;23:5570. doi: 10.3390/ijms23105570. PubMed DOI PMC
Axelrod H.D., Valkenburg K.C., Amend S.R., Hicks J.L., Parsana P., Torga G., De Marzo A.M., Pienta K.J. AXL Is a Putative Tumor Suppressor and Dormancy Regulator in Prostate Cancer. Mol. Cancer Res. 2019;17:356–369. doi: 10.1158/1541-7786.MCR-18-0718. PubMed DOI PMC
Feng Y., Duan T., Du Y., Jin S., Wang M., Cui J., Wang R.F. LRRC25 Functions as an Inhibitor of NF-κB Signaling Pathway by Promoting p65/RelA for Autophagic Degradation. Sci. Rep. 2017;7:1–12. doi: 10.1038/s41598-017-12573-3. PubMed DOI PMC
Chen Y., Cao B., Zheng W., Sun Y., Xu T. eIF3k inhibits NF-κB signaling by targeting MyD88 for ATG5-mediated autophagic degradation in teleost fish. J. Biol. Chem. 2022;298:101730. doi: 10.1016/j.jbc.2022.101730. PubMed DOI PMC
Tanimura A., Nakazato A., Tanaka N. MYD88 signals induce tumour-initiating cell generation through the NF-κB-HIF-1α activation cascade. Sci. Rep. 2021;11:3991. doi: 10.1038/s41598-021-83603-4. PubMed DOI PMC
Boudesco C., Verhoeyen E., Martin L., Chassagne-Clement C., Salmi L., Mhaidly R., Pangault C., Fest T., Ramla S., Jardin F., et al. HSP110 sustains chronic NF-κB signaling in activated B-cell diffuse large B-cell lymphoma through MyD88 stabilization. Blood. 2018;132:510–520. doi: 10.1182/blood-2017-12-819706. PubMed DOI
Poulain S., Roumier C., Decambron A., Renneville A., Herbaux C., Bertrand E., Tricot S., Daudignon A., Galiègue-Zouitina S., Soenen V., et al. MYD88 L265P mutation in Waldenstrom macroglobulinemia. Blood. 2013;121:4504–4511. doi: 10.1182/blood-2012-06-436329. PubMed DOI
Schafer A.R.M., Smith J.L., Pryke K.M., DeFilippis V.R., Hirsch A.J. The E3 Ubiquitin Ligase SIAH1 Targets MyD88 for Proteasomal Degradation During Dengue Virus Infection. Front. Microbiol. 2020;11:24. doi: 10.3389/fmicb.2020.00024. PubMed DOI PMC
Li Q., Wang F., Wang Q., Zhang N., Zheng J., Zheng M., Liu R., Cui H., Wen J., Zhao G. SPOP promotes ubiquitination and degradation of MyD88 to suppress the innate immune response. PLoS Pathog. 2020;16:e1008188. doi: 10.1371/journal.ppat.1008188. PubMed DOI PMC
Cohen P., Strickson S. The role of hybrid ubiquitin chains in the MyD88 and other innate immune signalling pathways. Cell Death Differ. 2017;24:1153–1159. doi: 10.1038/cdd.2017.17. PubMed DOI PMC
Yu X., Li W., Deng Q., Liu H., Wang X., Hu H., Cao Y., Xu-Monette Z.Y., Li L., Zhang M., et al. MYD88 L265P elicits mutation-specific ubiquitination to drive NF-κB activation and lymphomagenesis. Blood. 2021;137:1615–1627. doi: 10.1182/blood.2020004918. PubMed DOI PMC
Morman R.E., Schweickert P.G., Konieczny S.F., Taparowsky E.J. BATF regulates the expression of Nfil3, Wnt10a and miR155hg for efficient induction of antibody class switch recombination in mice. Eur. J. Immunol. 2018;48:1492. doi: 10.1002/eji.201747360. PubMed DOI PMC
Nogai H., Wenzel S.S., Hailfinger S., Grau M., Kaergel E., Seitz V., Wollert-Wulf B., Pfeifer M., Wolf A., Frick M., et al. IκB-ζ controls the constitutive NF-κB target gene network and survival of ABC DLBCL. Blood. 2013;122:2242–2250. doi: 10.1182/blood-2013-06-508028. PubMed DOI
Liu T., Zhang L., Joo D., Sun S.C. NF-κB signaling in inflammation. Signal Transduct. Target. Ther. 2017;2:1–9. doi: 10.1038/sigtrans.2017.23. PubMed DOI PMC
Guan S., Lu J., Zhao Y., Woodfield S.E., Zhang H., Xu X., Yu Y., Zhao J., Bieerkehazhi S., Liang H., et al. TAK1 inhibitor 5Z-7-oxozeaenol sensitizes cervical cancer to doxorubicin-induced apoptosis. Oncotarget. 2017;8:33666–33675. doi: 10.18632/oncotarget.16895. PubMed DOI PMC
Feng S., Wang K., Shao Z., Lin Q., Li B., Liu P. MiR-373/miR-520s-CD44 Axis Significantly Inhibits the Growth and Invasion of Human Glioblastoma Cells. Arch. Med Res. 2022;53:550–561. doi: 10.1016/j.arcmed.2022.08.003. PubMed DOI
Markasz L., Savani R.C., Jonzon A., Sindelar R. CD44 and RHAMM expression patterns in the human developing lung. Pediatr. Res. 2020;89:134–142. doi: 10.1038/s41390-020-0873-y. PubMed DOI
Zhang X., Yang L., Lei W., Hou Q., Huang M., Zhou R., Enver T., Wu S. Single-cell sequencing reveals CD133+CD44−-originating evolution and novel stemness related variants in human colorectal cancer. Ebiomedicine. 2022;82 doi: 10.1016/j.ebiom.2022.104125. PubMed DOI PMC
Zhang H., Brown R.L., Wei Y., Zhao P., Liu S., Liu X., Deng Y., Hu X., Zhang J., Gao X.D., et al. CD44 splice isoform switching determines breast cancer stem cell state. Genes Dev. 2019;33:166–179. doi: 10.1101/gad.319889.118. PubMed DOI PMC
He Y., Xue C., Yu Y., Chen J., Chen X., Ren F., Ren Z., Cui G., Sun R. CD44 is overexpressed and correlated with tumor progression in gallbladder cancer. Cancer Manag. Res. 2018;10:3857–3865. doi: 10.2147/CMAR.S175681. PubMed DOI PMC
Xu H., Niu M., Yuan X., Wu K., Liu A. CD44 as a tumor biomarker and therapeutic target. Exp. Hematol. Oncol. 2020;9:1–14. doi: 10.1186/s40164-020-00192-0. PubMed DOI PMC
Senbanjo L.T., Chellaiah M.A. CD44: A Multifunctional Cell Surface Adhesion Receptor Is a Regulator of Progression and Metastasis of Cancer Cells. Front. Cell Dev. Biol. 2017;5:18. doi: 10.3389/fcell.2017.00018. PubMed DOI PMC
Stauder R., Eisterer W., Thaler J., Gunthert U. CD44 variant isoforms in non-Hodgkin’s lymphoma: A new independent prognostic factor. Blood. 1995;85:2885–2899. doi: 10.1182/blood.V85.10.2885.bloodjournal85102885. PubMed DOI
Higashi M., Sugaya Y., Soeta S., Yokota A., Ishii G., Harigaya K. CD44 expression during tumor progression of follicular lymphoma. Oncol. Rep. 2009;22:1135–1140. doi: 10.3892/or_00000546. PubMed DOI
Espasa A., Tapia G., Vergara S., Raya M., Juncà J., Sorigue M. Flow cytometric expression of CD71, CD81, CD44 and CD39 in B cell lymphoma. Scand. J. Clin. Lab. Investig. 2021;81:413–417. doi: 10.1080/00365513.2021.1929446. PubMed DOI
Babst N., Isbell L.K., Rommel F., Tura A., Ranjbar M., Grisanti S., Tschuch C., Schueler J., Doostkam S., Reinacher P.C., et al. CXCR4, CXCR5 and CD44 May Be Involved in Homing of Lymphoma Cells into the Eye in a Patient Derived Xenograft Homing Mouse Model for Primary Vitreoretinal Lymphoma. Int. J. Mol. Sci. 2022;23:11757. doi: 10.3390/ijms231911757. PubMed DOI PMC
Eberth S., Schneider B., Rosenwald A., Hartmann E.M., Romani J., Zaborski M., Siebert R., Drexler H.G., Quentmeier H. Epigenetic regulation of CD44in Hodgkin and non-Hodgkin lymphoma. BMC Cancer. 2010;10:517. doi: 10.1186/1471-2407-10-517. PubMed DOI PMC
Wallach-Dayan S.B., Grabovsky V., Moll J., Sleeman J., Herrlich P., Alon R., Naor D. CD44-dependent lymphoma cell dissemination: A cell surface CD44 variant, rather than standard CD44, supports in vitro lymphoma cell rolling on hyaluronic acid substrate and its in vivo accumulation in the peripheral lymph nodes. J. Cell Sci. 2001;114:3463–3477. doi: 10.1242/jcs.114.19.3463. PubMed DOI
Lenz G., Wright G., Dave S.S., Xiao W., Powell J., Zhao H., Xu W., Tan B., Goldschmidt N., Iqbal J., et al. Stromal Gene Signatures in Large-B-Cell Lymphomas. N. Eng. J. Med. 2008;359:2313–2323. doi: 10.1056/NEJMoa0802885. PubMed DOI PMC
Cardesa-Salzmann T.M., Colomo L., Gutierrez G., Chan W.C., Weisenburger D., Climent F., González-Barca E., Mercadal S., Arenillas L., Serrano S., et al. High microvessel density determines a poor outcome in patients with diffuse large B-cell lymphoma treated with rituximab plus chemotherapy. Haematologica. 2011;96:996–1001. doi: 10.3324/haematol.2010.037408. PubMed DOI PMC
Prescott J.A., Mitchell J.P., Cook S.J. Inhibitory feedback control of NF-κB signalling in health and disease. Biochem. J. 2021;478:2619. doi: 10.1042/BCJ20210139. PubMed DOI PMC
Ruland J. Return to Homeostasis: Downregulation of NF-ΚB Responses. Nat Immunol. 2011;12:709–714. doi: 10.1038/ni.2055. PubMed DOI
Wenzl K., Manske M.K., Sarangi V., Asmann Y.W., Greipp P.T., Schoon H.R., Braggio E., Maurer M.J., Feldman A.L., Witzig T.E., et al. Loss of TNFAIP3 enhances MYD88L265P-driven signaling in non-Hodgkin lymphoma. Blood Cancer J. 2018;8:97. doi: 10.1038/s41408-018-0130-3. PubMed DOI PMC
Choi J.W., Kim Y., Lee J.H., Kim Y.S. MYD88 expression and L265P mutation in diffuse large B-cell lymphoma. Hum. Pathol. 2013;44:1375–1381. doi: 10.1016/j.humpath.2012.10.026. PubMed DOI
Lacy S.E., Barrans S.L., Beer P.A., Painter D., Smith A.G., Roman E., Cooke S.L., Ruiz C., Glover P., Van Hoppe S.J.L., et al. Targeted sequencing in DLBCL, molecular subtypes, and outcomes: A Haematological Malignancy Research Network report. Blood. 2020;135:1759–1771. doi: 10.1182/blood.2019003535. PubMed DOI PMC
Wang J., Zhang G., Sui Y., Yang Z., Chu Y., Tang H., Guo B., Zhang C., Wu C. CD52 Is a Prognostic Biomarker and Associated with Tumor Microenvironment in Breast Cancer. Front. Genet. 2020;11 doi: 10.3389/fgene.2020.578002. PubMed DOI PMC
Rodig S.J., Abramson J.S., Pinkus G.S., Treon S.P., Dorfman D.M., Dong H.Y., Shipp M.A., Kutok J.L. Heterogeneous CD52 Expression among Hematologic Neoplasms: Implications for the Use of Alemtuzumab (CAMPATH-1H) Clin. Cancer Res. 2006;12:7174–7179. doi: 10.1158/1078-0432.CCR-06-1275. PubMed DOI
Craig J.W., Mina M.J., Crombie J.L., LaCasce A.S., Weinstock D.M., Pinkus G.S., Pozdnyakova O. Assessment of CD52 expression in "double-hit" and "double-expressor" lymphomas: Implications for clinical trial eligibility. PLoS ONE. 2018;13:e0199708. doi: 10.1371/journal.pone.0199708. PubMed DOI PMC
Teo E.C.Y., Chew Y., Phipps C. A review of monoclonal antibody therapies in lymphoma. Crit. Rev. Oncol. 2016;97:1–10. doi: 10.1016/j.critrevonc.2015.08.014. PubMed DOI
Matsushita M., Yamazaki R., Ikeda H., Kawakami Y. Preferentially Expressed Antigen of Melanoma (PRAME) in the Development of Diagnostic and Therapeutic Methods for Hematological Malignancies. Leuk. Lymphoma. 2003;44:439–444. doi: 10.1080/1042819021000035725. PubMed DOI
Wadelin F., Fulton J., McEwan P.A., Spriggs K.A., Emsley J., Heery D.M. Leucine-rich repeat protein PRAME: Expression, potential functions and clinical implications for leukaemia. Mol. Cancer. 2010;9:226. doi: 10.1186/1476-4598-9-226. PubMed DOI PMC
Kewitz S., Staege M.S. Knock-Down of PRAME Increases Retinoic Acid Signaling and Cytotoxic Drug Sensitivity of Hodgkin Lymphoma Cells. PLoS ONE. 2013;8:e55897. doi: 10.1371/journal.pone.0055897. PubMed DOI PMC
Weber G., Caruana I., Rouce R.H., Barrett A.J., Gerdemann U., Leen A.M., Rabin K.R., Bollard C.M. Generation of Tumor Antigen-Specific T Cell Lines from Pediatric Patients with Acute Lymphoblastic Leukemia—Implications for Immunotherapy. Clin. Cancer Res. 2013;19:5079–5091. doi: 10.1158/1078-0432.CCR-13-0955. PubMed DOI PMC
Pujol J.L., De Pas T., Rittmeyer A., Vallières E., Kubisa B., Levchenko E., Wiesemann S., Masters G.A., Shen R., Tjulandin S.A., et al. Safety and Immunogenicity of the PRAME Cancer Immunotherapeutic in Patients with Resected Non–Small Cell Lung Cancer: A Phase I Dose Escalation Study. J. Thorac. Oncol. 2016;11:2208–2217. doi: 10.1016/j.jtho.2016.08.120. PubMed DOI
Orlando D., Miele E., de Angelis B., Guercio M., Boffa I., Sinibaldi M., Po A., Caruana I., Abballe L., Carai A., et al. Adoptive Immunotherapy Using PRAME-Specific T Cells in Medulloblastoma. Cancer Res. 2018;78:3337–3349. doi: 10.1158/0008-5472.CAN-17-3140. PubMed DOI
Sun Z., Wu Z., Zhang F., Guo Q., Li L., Li K., Chen H., Zhao J., Song D., Huang Q., et al. Prame is critical for breast cancer growth and metastasis. Gene. 2016;594:160–164. doi: 10.1016/j.gene.2016.09.016. PubMed DOI
Takata K., Chong L.C., Ennishi D., Aoki T., Li M.Y., Thakur A., Healy S., Viganò E., Dao T., Kwon D., et al. Tumor-associated antigen PRAME exhibits dualistic functions that are targetable in diffuse large B cell lymphoma. J. Clin. Investig. 2022;132 doi: 10.1172/JCI145343. PubMed DOI PMC
Martincic K., Alkan S.A., Cheatle A., Borghesi L., Milcarek C. Transcription elongation factor ELL2 directs immunoglobulin secretion in plasma cells by stimulating altered RNA processing. Nat. Immunol. 2009;10:1102–1109. doi: 10.1038/ni.1786. PubMed DOI PMC
Park K.S., Bayles I., Szlachta-McGinn A., Paul J., Boiko J., Santos P., Liu J., Wang Z., Borghesi L., Milcarek C. Transcription Elongation Factor ELL2 Drives Ig Secretory-Specific mRNA Production and the Unfolded Protein Response. J. Immunol. 2014;193:4663–4674. doi: 10.4049/jimmunol.1401608. PubMed DOI PMC
Chen Y., Vos S.M., Dienemann C., Ninov M., Urlaub H., Cramer P. Allosteric transcription stimulation by RNA polymerase II super elongation complex. Mol. Cell. 2021;81:3386–3399.e10. doi: 10.1016/j.molcel.2021.06.019. PubMed DOI
Care M., Barrans S., Worrillow L., Jack A., Westhead D.R., Tooze R.M. A Microarray Platform-Independent Classification Tool for Cell of Origin Class Allows Comparative Analysis of Gene Expression in Diffuse Large B-cell Lymphoma. PLoS ONE. 2013;8:e55895. doi: 10.1371/journal.pone.0055895. PubMed DOI PMC
Tran D.Q., Andersson J., Wang R., Ramsey H., Unutmaz D., Shevach E.M. GARP (LRRC32) is essential for the surface expression of latent TGF-β on platelets and activated FOXP3 + regulatory T cells. Proc. Natl. Acad. Sci. USA. 2009;106:13445–13450. doi: 10.1073/pnas.0901944106. PubMed DOI PMC
Wallace C.H., Wu B.X., Salem M., Ansa-Addo E.A., Metelli A., Sun S., Gilkeson G., Shlomchik M.J., Liu B., Li Z. B lymphocytes confer immune tolerance via cell surface GARP-TGF-β complex. J. Clin. Investig. 2018;3:e99863. doi: 10.1172/jci.insight.99863. PubMed DOI PMC
Bouchard A., Collin B., Garrido C., Bellaye P.S., Kohli E. GARP: A Key Target to Evaluate Tumor Immunosuppressive Microenvironment. Biology. 2021;10:836. doi: 10.3390/biology10090836. PubMed DOI PMC
Zimmer N., Trzeciak E.R., Graefen B., Satoh K., Tuettenberg A. GARP as a Therapeutic Target for the Modulation of Regulatory T Cells in Cancer and Autoimmunity. Front. Immunol. 2022;13:928450. doi: 10.3389/fimmu.2022.928450. PubMed DOI PMC
Carrillo-Gálvez A.B., Quintero J.E., Rodríguez R., Menéndez S.T., González M.V., Blanco-Lorenzo V., Allonca E., Farias V.D.A., González-Correa J.E., Erill-Sagalés N., et al. GARP promotes the proliferation and therapeutic resistance of bone sarcoma cancer cells through the activation of TGF-β. Cell Death Dis. 2020;11:1–12. doi: 10.1038/s41419-020-03197-z. PubMed DOI PMC
Metelli A., Wu B.X., Fugle C.W., Rachidi S., Sun S., Zhang Y., Wu J., Tomlinson S., Howe P.H., Yang Y., et al. Surface Expression of TGFβ Docking Receptor GARP Promotes Oncogenesis and Immune Tolerance in Breast Cancer. Cancer Res. 2016;76:7106–7117. doi: 10.1158/0008-5472.CAN-16-1456. PubMed DOI PMC
Li A., Chang Y., Song N.J., Wu X., Chung D., Riesenberg B.P., Velegraki M., Giuliani G.D., Das K., Okimoto T., et al. Selective targeting of GARP-LTGFβ axis in the tumor microenvironment augments PD-1 blockade via enhancing CD8+ T cell antitumor immunity. J. Immunother. Cancer. 2022;10:e005433. doi: 10.1136/jitc-2022-005433. PubMed DOI PMC
Korbecki J., Kojder K., Simińska D., Bohatyrewicz R., Gutowska I., Chlubek D., Baranowska-Bosiacka I. CC Chemokines in a Tumor: A Review of Pro-Cancer and Anti-Cancer Properties of the Ligands of Receptors CCR1, CCR2, CCR3, and CCR4. Int. J. Mol. Sci. 2020;21:8412. doi: 10.3390/ijms21218412. PubMed DOI PMC
Niens M., Visser L., Nolte I.M., van der Steege G., Diepstra A., Cordano P., Jarrett R.F., Meerman G.J.T., Poppema S., Van Der Berg A. Serum chemokine levels in Hodgkin lymphoma patients: Highly increased levels of CCL17 and CCL22. Br. J. Haematol. 2008;140:527–536. doi: 10.1111/j.1365-2141.2007.06964.x. PubMed DOI
Kumai T., Nagato T., Kobayashi H., Komabayashi Y., Ueda S., Kishibe K., Ohkuri T., Takahara M., Celis E., Harabuchi Y. CCL17 and CCL22/CCR4 signaling is a strong candidate for novel targeted therapy against nasal natural killer/T-cell lymphoma. Cancer Immunol. Immunother. 2015;64:697. doi: 10.1007/s00262-015-1675-7. PubMed DOI PMC
Döring C., Hansmann M.L., Agostinelli C., Piccaluga P.P., Facchetti F., Pileri S., Küppers R., Newrzela S., Hartmann S. A novel immunohistochemical classifier to distinguish Hodgkin lymphoma from ALK anaplastic large cell lymphoma. Mod. Pathol. 2014;27:1345–1354. doi: 10.1038/modpathol.2014.44. PubMed DOI
Takegawa S., Jin Z., Nakayama T., Oyama T., Hieshima K., Nagakubo D., Shirakawa A.K., Tsuzuki T., Nakamura S., Yoshie O. Expression of CCL17 and CCL22 by latent membrane protein 1-positive tumor cells in age-related Epstein–Barr virus-associated B-cell lymphoproliferative disorder. Cancer Sci. 2008;99:296–302. doi: 10.1111/j.1349-7006.2007.00687.x. PubMed DOI PMC
Zeng Q., Gupta A., Xin L., Poon M., Schwarz H. Plasma Factors for the Differentiation of Hodgkin’s Lymphoma and Diffused Large B Cell Lymphoma and for Monitoring Remission. J. Hematol. 2019;8:47–54. doi: 10.14740/jh499. PubMed DOI PMC
Murphy T.L., Tussiwand R., Murphy K.M. Specificity through cooperation: BATF–IRF interactions control immune-regulatory networks. Nat. Rev. Immunol. 2013;13:499–509. doi: 10.1038/nri3470. PubMed DOI
Betz B.C., Jordan-Williams K.L., Wang C., Kang S.G., Liao J., Logan M.R., Kim C.H., Taparowsky E.J. Batf coordinates multiple aspects of B and T cell function required for normal antibody responses. J. Exp. Med. 2010;207:933–942. doi: 10.1084/jem.20091548. PubMed DOI PMC
Kurachi M., Barnitz R.A., Yosef N., Odorizzi P.M., A DiIorio M., E Lemieux M., Yates K., Godec J., Klatt M.G., Regev A., et al. The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells. Nat. Immunol. 2014;15:373. doi: 10.1038/ni.2834. PubMed DOI PMC
Sahoo A., Alekseev A., Tanaka K., Obertas L., Lerman B., Haymaker C., Clise-Dwyer K., McMurray J.S., Nurieva R. Batf is important for IL-4 expression in T follicular helper cells. Nat. Commun. 2015;6:1–10. doi: 10.1038/ncomms8997. PubMed DOI PMC
Schleussner N., Merkel O., Costanza M., Liang H.C., Hummel F., Romagnani C., Durek P., Anagnostopoulos I., Hummel M., Jöhrens K., et al. The AP-1-BATF and -BATF3 module is essential for growth, survival and TH17/ILC3 skewing of anaplastic large cell lymphoma. Leukemia. 2018;32:1994. doi: 10.1038/s41375-018-0045-9. PubMed DOI PMC
Seo H., González-Avalos E., Zhang W., Ramchandani P., Yang C., Lio C.-W.J., Rao A., Hogan P.G. BATF and IRF4 cooperate to counter exhaustion in tumor-infiltrating CAR T cells. Nat. Immunol. 2021;22:983–995. doi: 10.1038/s41590-021-00964-8. PubMed DOI PMC
Ise W., Kohyama M., Schraml B., Zhang T., Schwer B., Basu U., Alt F.W., Tang J., Oltz E.M., Murphy T.L., et al. The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T cells. Nat. Immunol. 2011;12:536–543. doi: 10.1038/ni.2037. PubMed DOI PMC
Sopel N., Graser A., Mousset S., Finotto S. The transcription factor BATF modulates cytokine-mediated responses in T cells. Cytokine Growth Factor Rev. 2016;30:39–45. doi: 10.1016/j.cytogfr.2016.03.004. PubMed DOI
Liao J., Humphrey S.E., Poston S., Taparowsky E.J. Batf Promotes Growth Arrest and Terminal Differentiation of Mouse Myeloid Leukemia Cells. Mol. Cancer Res. 2011;9:350. doi: 10.1158/1541-7786.MCR-10-0375. PubMed DOI PMC
Jia C., Ma Y., Wang M., Liu W., Tang F., Chen J. Evidence of Omics, Immune Infiltration, and Pharmacogenomics for BATF in a Pan-Cancer Cohort. Front. Mol. Biosci. 2022;9:392. doi: 10.3389/fmolb.2022.844721. PubMed DOI PMC
Care M., Cocco M., Laye J.P., Barnes N., Huang Y., Wang M., Barrans S., Du M., Jack A., Westhead D., et al. SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity. Nucleic Acids Res. 2014;42:7591–7610. doi: 10.1093/nar/gku451. PubMed DOI PMC
Rouillard A.D., Gundersen G.W., Fernandez N.F., Wang Z., Monteiro C.D., McDermott M.G., Ma’Ayan A. The harmonizome: A collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database. 2016;2016:100. doi: 10.1093/database/baw100. PubMed DOI PMC
Schuster M., Annemann M., Plaza-Sirvent C., Schmitz I. Atypical IκB Proteins - Nuclear Modulators of NF-ΚB Signaling. Cell Commun. Signal. 2013;11:1–11. doi: 10.1186/1478-811X-11-23. PubMed DOI PMC
Willems M., Dubois N., Musumeci L., Bours V., Robe P.A. IκBζ: An emerging player in cancer. Oncotarget. 2016;7:66310. doi: 10.18632/oncotarget.11624. PubMed DOI PMC
Gautam P., Maenner S., Cailotto F., Reboul P., Labialle S., Jouzeau J., Bourgaud F., Moulin D. Emerging role of IκBζ in inflammation: Emphasis on psoriasis. Clin. Transl. Med. 2022;12:e1032. doi: 10.1002/ctm2.1032. PubMed DOI PMC
Motoyama M., Yamazaki S., Eto-Kimura A., Takeshige K., Muta T. Positive and Negative Regulation of Nuclear Factor-κB-mediated Transcription by IκB-ζ, an Inducible Nuclear Protein. J. Biol. Chem. 2005;280:7444–7451. doi: 10.1074/jbc.M412738200. PubMed DOI
Xu T., Rao T., Yu W.M., Ning J.Z., Yu X., Zhu S.M., Yang K., Bai T., Cheng F. Upregulation of NFKBIZ affects bladder cancer progression via the PTEN/PI3K/Akt signaling pathway. Int. J. Mol. Med. 2021;47:1–12. doi: 10.3892/ijmm.2021.4942. PubMed DOI PMC
Lenz G., Wright G.W., Emre N.C.T., Kohlhammer H., Dave S.S., Davis R.E., Carty S., Lam L.T., Shaffer A.L., Xiao W., et al. Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways. Proc. Natl. Acad. Sci. USA. 2008;105:13520. doi: 10.1073/pnas.0804295105. PubMed DOI PMC
Arthur S.E., Thomas N., Rushton C., Tang J., Alcaide M., Healy S., Telenius A., Mottok A., Scott D.W., Steidl C., et al. Nfkbiz 3′ UTR Mutations Confer Selective Growth Advantage and Affect Drug Response in Diffuse Large B-Cell Lymphoma. Blood. 2020;136:31. doi: 10.1182/blood-2020-137700. DOI
Arthur S.E., Jiang A., Grande B.M., Alcaide M., Cojocaru R., Rushton C.K., Mottok A., Hilton L.K., Lat P.K., Zhao E.Y., et al. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat. Commun. 2018;9:4001. doi: 10.1038/s41467-018-06354-3. PubMed DOI PMC
Hanihara F., Takahashi Y., Okuma A., Ohba T., Muta T. Transcriptional and post-transcriptional regulation of IκB-ζ upon engagement of the BCR, TLRs and FcγR. Int. Immunol. 2013;25:531–544. doi: 10.1093/intimm/dxt017. PubMed DOI
Pricci F., Leto G., Amadio L., Iacobini C., Romeo G., Cordone S., Gradini R., Barsotti P., Liu F.T., Di Mario U., et al. Role of galectin-3 as a receptor for advanced glycosylation end products. Kidney Int. 2000;77:S31–S39. doi: 10.1046/j.1523-1755.2000.07706.x. PubMed DOI
Sciacchitano S., Lavra L., Morgante A., Ulivieri A., Magi F., De Francesco G.P., Bellotti C., Salehi L.B., Ricci A. Galectin-3: One Molecule for an Alphabet of Diseases, from A to Z. Int. J. Mol. Sci. 2018;19:379. doi: 10.3390/ijms19020379. PubMed DOI PMC
Díaz-Alvarez L., Ortega E. The Many Roles of Galectin-3, a Multifaceted Molecule, in Innate Immune Responses against Pathogens. Mediat. Inflamm. 2017;2017:1–10. doi: 10.1155/2017/9247574. PubMed DOI PMC
Nangia-Makker P., Hogan V., Raz A. Galectin-3 and cancer stemness. Glycobiology. 2018;28:172–181. doi: 10.1093/glycob/cwy001. PubMed DOI PMC
Ruvolo P.P. Galectin 3 as a guardian of the tumor microenvironment. Biochim. et Biophys. Acta (BBA)-Mol. Cell Res. 2016;1863:427–437. doi: 10.1016/j.bbamcr.2015.08.008. PubMed DOI
Dong R., Zhang M., Hu Q., Zheng S., Soh A., Zheng Y., Yuan H. Galectin-3 as a novel biomarker for disease diagnosis and a target for therapy (Review) Int. J. Mol. Med. 2018;41:599–614. doi: 10.3892/ijmm.2017.3311. PubMed DOI PMC
Ruvolo P.P., Hu C.W., Qiu Y., Ruvolo V.R., Go R.L., Hubner S.E., Coombes K.R., Andreeff M., Qutub A.A., Kornblau S.M. LGALS3 is connected to CD74 in a previously unknown protein network that is associated with poor survival in patients with AML. Ebiomedicine. 2019;44:126–137. doi: 10.1016/j.ebiom.2019.05.025. PubMed DOI PMC
Michalová Z., Čoma M., Kičová M., Gabzdilová J., Dedinská K., Guman T., Hájiková M., Veselinyová D., Giertlova M., Gál P., et al. Overexpression of Galectin-3 in Chronic Lymphocytic Leukemia Is Associated With 17p Deletion: A Short Report. Anticancer. Res. 2019;39:2805–2810. doi: 10.21873/anticanres.13408. PubMed DOI
Koh Y.W., Jung S.J., Park C.S., Yoon D.H., Suh C., Huh J. LGALS3 as a prognostic factor for classical Hodgkin’s lymphoma. Mod. Pathol. 2014;27:1338–1344. doi: 10.1038/modpathol.2014.38. PubMed DOI
Shipp M.A., Ross K.N., Tamayo P., Weng A.P., Aguiar R.C.T., Gaasenbeek M., Angelo M., Reich M., Pinkus G.S., Ray T.S., et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat. Med. 2002;8:68–74. doi: 10.1038/nm0102-68. PubMed DOI
Shi Y., Tang D., Li X., Xie X., Ye Y., Wang L. Galectin Family Members: Emerging Novel Targets for Lymphoma Therapy? Front. Oncol. 2022;12:2092. doi: 10.3389/fonc.2022.889034. PubMed DOI PMC
Pena C., Mirandola L., Figueroa J.A., Hosiriluck N., Suvorava N., Trotter K., Reidy A., Rakhshanda R., Payne D., Jenkins M., et al. Galectins as therapeutic targets for hematological malignancies: A hopeful sweetness. Ann. Transl. Med. 2014;2:87. doi: 10.3978/j.issn.2305-5839.2014.09.14. PubMed DOI PMC
Clark M.C., Pang M., Hsu D.K., Liu F.T., de Vos S., Gascoyne R.D., Said J., Baum L.G. Galectin-3 binds to CD45 on diffuse large B-cell lymphoma cells to regulate susceptibility to cell death. Blood. 2012;120:4635–4644. doi: 10.1182/blood-2012-06-438234. PubMed DOI PMC
Hoyer K.K., Pang M., Gui D., Shintaku I.P., Kuwabara I., Liu F.T., Said J.W., Baum L.G., Teitell M.A. An Anti-Apoptotic Role for Galectin-3 in Diffuse Large B-Cell Lymphomas. Am. J. Pathol. 2004;164:893–902. doi: 10.1016/S0002-9440(10)63177-X. PubMed DOI PMC
André U., Dictor M., Jerkeman M., Berglund M., Sundström C., Linderoth J., Rosenquist R., Borrebaeck C.A.K., Ek S. Identification of molecular targets associated with transformed diffuse large B cell lymphoma using highly purified tumor cells. Am. J. Hematol. 2009;84:803–808. doi: 10.1002/ajh.21549. PubMed DOI
Kim S.J., Lee S.J., Sung H.J., Choi I.K., Choi C.W., Kim B.S., Kim J.S., Yu W., Hwang H.S., Kim I.S. Increased Serum 90K and Galectin-3 Expression Are Associated with Advanced Stage and a Worse Prognosis in Diffuse Large B-Cell Lymphomas. Acta Haematol. 2008;120:211–216. doi: 10.1159/000193223. PubMed DOI
FDA approves anti-LAG3 checkpoint. Nat. Biotechnol. 2022;40:625. doi: 10.1038/s41587-022-01331-0. PubMed DOI
Bae J., Accardi F., Hideshima T., Tai Y.T., Prabhala R., Shambley A., Wen K., Rowell S., Richardson P.G., Munshi N.C., et al. Targeting LAG3/GAL-3 to overcome immunosuppression and enhance anti-tumor immune responses in multiple myeloma. Leukemia. 2021;36:138–154. doi: 10.1038/s41375-021-01301-6. PubMed DOI PMC
Nakajima K., Balan V., Raz A. Galectin-3: An immune checkpoint target for musculoskeletal tumor patients. Cancer Metastasis Rev. 2020;40:297–302. doi: 10.1007/s10555-020-09932-4. PubMed DOI PMC
Yan Y., Zuo X., Wei D. Concise Review: Emerging Role of CD44 in Cancer Stem Cells: A Promising Biomarker and Therapeutic Target. STEM CELLS Transl. Med. 2015;4:1033–1043. doi: 10.5966/sctm.2015-0048. PubMed DOI PMC
Thapa R., Wilson G.D. The Importance of CD44 as a Stem Cell Biomarker and Therapeutic Target in Cancer. Stem Cells Int. 2016;2016:1–15. doi: 10.1155/2016/2087204. PubMed DOI PMC
Goodison S., Urquidi V., Tarin D. CD44 Cell Adhesion Molecules. J. Clin. Pathol. Mol. Pathol. 1999;52:189–196. doi: 10.1136/mp.52.4.189. PubMed DOI PMC
Batsché E., Yi J., Mauger O., Kornobis E., Hopkins B., Hanmer-Lloyd C., Muchardt C. CD44 alternative splicing senses intragenic DNA methylation in tumors via direct and indirect mechanisms. Nucleic Acids Res. 2021;49:6213–6237. doi: 10.1093/nar/gkab437. PubMed DOI PMC
Prochazka L., Tesarik R., Turanek J. Regulation of alternative splicing of CD44 in cancer. Cell. Signal. 2014;26:2234–2239. doi: 10.1016/j.cellsig.2014.07.011. PubMed DOI
Dingemans K.P., Ramkema M.D., Pals S.T. CD44 Is Exposed to the Extracellular Matrix at Invasive Sites in Basal Cell Carcinomas. Lab. Investig. 2002;82:313–322. doi: 10.1038/labinvest.3780425. PubMed DOI
Hertweck M.K., Erdfelder F., Kreuzer K.A. CD44 in hematological neoplasias. Ann. Hematol. 2011;90:493–508. doi: 10.1007/s00277-011-1161-z. PubMed DOI
Huang W.Y., Lin J.N., Hsieh J.T., Chou S.C., Lai C.H., Yun E.J., Lo U.G., Pong R.C., Lin J.H., Lin Y.H. Nanoparticle Targeting CD44-Positive Cancer Cells for Site-Specific Drug Delivery in Prostate Cancer Therapy. ACS Appl. Mater. Interfaces. 2016;8:30722–30734. doi: 10.1021/acsami.6b10029. PubMed DOI
Orian-Rousseau V., Ponta H. Perspectives of CD44 targeting therapies. Arch. Toxicol. 2014;89:3–14. doi: 10.1007/s00204-014-1424-2. PubMed DOI
Hsiao Y.W., Chi J.Y., Li C.F., Chen L.Y., Chen Y.T., Liang H.Y., Lo Y.C., Hong J.Y., Chuu C.P., Hung L.Y., et al. Disruption of the pentraxin 3/CD44 interaction as an efficient therapy for triple-negative breast cancers. Clin. Transl. Med. 2022;12:e724. doi: 10.1002/ctm2.724. PubMed DOI PMC
Reimann M., Schrezenmeier J.F., Richter-Pechanska P., Dolnik A., Hick T.P., Schleich K., Cai X., Fan D.N.Y., Lohneis P., Masswig S., et al. Adaptive T-cell immunity controls senescence-prone MyD88- or CARD11-mutant B-cell lymphomas. Blood. 2021;137:2785–2799. doi: 10.1182/blood.2020005244. PubMed DOI
Hardee J., Ouyang Z., Zhang Y., Kundaje A., Lacroute P., Snyder M. STAT3 Targets Suggest Mechanisms of Aggressive Tumorigenesis in Diffuse Large B-Cell Lymphoma. G3 (Bethesda) 2013;3:2173–2185. doi: 10.1534/g3.113.007674. PubMed DOI PMC
Nørgaard C.H., Jakobsen L.H., Gentles A.J., Dybkær K., El-Galaly T.C., Bødker J.S., Schmitz A., Johansen P., Herold T., Spiekermann K., et al. Subtype assignment of CLL based on B-cell subset associated gene signatures from normal bone marrow – A proof of concept study. PLoS ONE. 2018;13:e0193249. doi: 10.1371/journal.pone.0193249. PubMed DOI PMC
Dybkær K., Bøgsted M., Falgreen S., Bødker J.S., Kjeldsen M.K., Schmitz A., Bilgrau A.E., Xu-Monette Z.Y., Li L., Bergkvist K.S., et al. Diffuse Large B-Cell Lymphoma Classification System That Associates Normal B-Cell Subset Phenotypes with Prognosis. J. Clin. Oncol. 2015;33:1379–1388. doi: 10.1200/JCO.2014.57.7080. PubMed DOI PMC
Frei E., Visco C., Xu-Monette Z.Y., Dirnhofer S., Dybkær K., Orazi A., Bhagat G., Hsi E.D., van Krieken J.H., Ponzoni M., et al. Addition of rituximab to chemotherapy overcomes the negative prognostic impact of cyclin E expression in diffuse large B-cell lymphoma. J. Clin. Pathol. 2013;66:956–961. doi: 10.1136/jclinpath-2013-201619. PubMed DOI
NF-KB Target Genes NF-KB Transcription Factors Boston University. [(accessed on 29 January 2023)]. Available online: https://www.bu.edu/nf-kb/gene-resources/target-genes/
Xue X., Zeng N., Gao Z., Du M.Q. Diffuse large B-cell lymphoma: Sub-classification by massive parallel quantitative RT-PCR. Lab. Investig. 2015;95:113–120. doi: 10.1038/labinvest.2014.136. PubMed DOI
Mölder F., Jablonski K.P., Letcher B., Hall M.B., Tomkins-Tinch C.H., Sochat V., Forster J., Lee S., Twardziok S.O., Kanitz A., et al. Sustainable data analysis with Snakemake. F1000Research. 2021;10:33. doi: 10.12688/f1000research.29032.2. PubMed DOI PMC
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011;17:10. doi: 10.14806/ej.17.1.200. DOI
Kopylova E., Noé L., Touzet H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–3217. doi: 10.1093/bioinformatics/bts611. PubMed DOI
Dobin A., Davis C.A., Schlesinger F., Drenkow J., Zaleski C., Jha S., Batut P., Chaisson M., Gingeras T.R. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21. doi: 10.1093/bioinformatics/bts635. PubMed DOI PMC
García-Alcalde F., Okonechnikov K., Carbonell J., Cruz L.M., Götz S., Tarazona S., Dopazo J., Meyer T.F., Conesa A. Qualimap: Evaluating next-generation sequencing alignment data. Bioinformatics. 2012;28:2678–2679. doi: 10.1093/bioinformatics/bts503. PubMed DOI
Love M.I., Huber W., Anders S. Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2. Genome Biol. 2014;15:1–21. doi: 10.1186/s13059-014-0550-8. PubMed DOI PMC
Wickham H. Ggplot2. Wiley Interdiscip. Rev. Comput. Stat. 2016;3:180–185. doi: 10.1002/wics.147. DOI
Budczies J., Klauschen F., Sinn B.V., Gyorffy B., Schmitt W.D., Darb-Esfahani S., Denkert C. Cutoff Finder: A Comprehensive and Straightforward Web Application Enabling Rapid Biomarker Cutoff Optimization. PLoS ONE. 2012;7:e51862. doi: 10.1371/journal.pone.0051862. PubMed DOI PMC
Leyva-Vega M., Gerfen J., Thiel B.D., Jurkiewicz D., Rand E.B., Pawlowska J., Kaminska D., Russo P., Gai X., Krantz I.D., et al. Genomic alterations in biliary atresia suggest region of potential disease susceptibility in 2q37.3. Am. J. Med Genet. Part A. 2010;152A:886–895. doi: 10.1002/ajmg.a.33332. PubMed DOI PMC
Wang F., Qin G., Liu J., Wang X., Ye B. Integrated Genome-Wide Methylation and Expression Analyses Reveal Key Regulators in Osteosarcoma. Comput. Math. Methods Med. 2020;2020:1–11. doi: 10.1155/2020/7067649. PubMed DOI PMC
Ye Y., Ma J., Zhang Q., Xiong K., Zhang Z., Chen C., Xiao H., Wang D. A CTL/M2 macrophage-related four-gene signature predicting metastasis-free survival in triple-negative breast cancer treated with adjuvant radiotherapy. Breast Cancer Res. Treat. 2021;190:329–341. doi: 10.1007/s10549-021-06379-1. PubMed DOI
Willer T., Prados B., Falcón-Pérez J.M., Renner-Müller I., Przemeck G.K.H., Lommel M., Coloma A., Valero M.C., de Angelis M.H., Tanner W., et al. Targeted disruption of the Walker–Warburg syndrome gene Pomt1 in mouse results in embryonic lethality. Proc. Natl. Acad. Sci. 2004;101:14126–14131. doi: 10.1073/pnas.0405899101. PubMed DOI PMC
Jaeken J. Congenital disorders of glycosylation. Handb Clin Neurol. 2013;113:1737–1743. doi: 10.1016/b978-0-444-59565-2.00044-7. PubMed DOI
Alonso-Rangel L., Benítez-Guerrero T., Martínez-Vieyra I., Cisneros B., Martínez-Tovar A., Winder S.J., Cerecedo D. A role for dystroglycan in the pathophysiology of acute leukemic cells. Life Sci. 2017;182:1–9. doi: 10.1016/j.lfs.2017.06.004. PubMed DOI
Quereda C., Pastor A., Martín-Nieto J. Involvement of abnormal dystroglycan expression and matriglycan levels in cancer pathogenesis. Cancer Cell Int. 2022;22:1–30. doi: 10.1186/s12935-022-02812-7. PubMed DOI PMC
Wloga D., Webster D.M., Rogowski K., Bré M.H., Levilliers N., Jerka-Dziadosz M., Janke C., Dougan S.T., Gaertig J. TTLL3 Is a Tubulin Glycine Ligase that Regulates the Assembly of Cilia. Dev. Cell. 2009;16:867–876. doi: 10.1016/j.devcel.2009.04.008. PubMed DOI
Meár L., Sutantiwanichkul T., Östman J., Damdimopoulou P., Lindskog C. Spatial Proteomics for Further Exploration of Missing Proteins: A Case Study of the Ovary. J. Proteome Res. 2022 doi: 10.1021/acs.jproteome.2c00392. PubMed DOI PMC
Yang J., Liu X., Yue G., Adamian M., Bulgakov O., Li T. Rootletin, a novel coiled-coil protein, is a structural component of the ciliary rootlet. J. Cell Biol. 2002;159:431–440. doi: 10.1083/jcb.200207153. PubMed DOI PMC
Ko D., Kim J., Rhee K., Choi H.-J. Identification of a Structurally Dynamic Domain for Oligomer Formation in Rootletin. J. Mol. Biol. 2020;432:3915–3932. doi: 10.1016/j.jmb.2020.04.012. PubMed DOI
Bahe S., Stierhof Y.D., Wilkinson C., Leiss F., Nigg E.A. Rootletin forms centriole-associated filaments and functions in centrosome cohesion. J. Cell Biol. 2005;171:27–33. doi: 10.1083/jcb.200504107. PubMed DOI PMC
Fabbri L., Bost F., Mazure N.M. Primary Cilium in Cancer Hallmarks. Int. J. Mol. Sci. 2019;20:1336. doi: 10.3390/ijms20061336. PubMed DOI PMC
Higgins M., Obaidi I., McMorrow T. Primary cilia and their role in cancer (Review) Oncol. Lett. 2019;17:3041–3047. doi: 10.3892/ol.2019.9942. PubMed DOI PMC
Blümel L., Qin N., Berlandi J., Paisana E., Cascão R., Custódia C., Pauck D., Picard D., Langini M., Stühler K., et al. Primary cilia contribute to the aggressiveness of atypical teratoid/rhabdoid tumors. Cell Death. Dis. 2022;13:1–13. doi: 10.1038/s41419-022-05243-4. PubMed DOI PMC
Wang J., Liu Y., Yang Z., Sui Y., Tian J., Tao L., Yao J., Wu C. CD52 Is a Prognostic Biomarker and Correlated with Immune Features in Breast Cancer. Res. Sq. 2020 doi: 10.21203/rs.3.rs-31586/v1. DOI
Hochgreb-Hägele T., Koo D.E., Bronner M.E. Znf385C mediates a novel p53-dependent transcriptional switch to control timing of facial bone formation. Dev. Biol. 2015;400:23–32. doi: 10.1016/j.ydbio.2015.01.011. PubMed DOI
Costessi A., Mahrour N., Tijchon E., Stunnenberg R., Stoel M.A., Jansen P.W., Sela D., Martin-Brown S., Washburn M., Florens L., et al. The tumour antigen PRAME is a subunit of a Cul2 ubiquitin ligase and associates with active NFY promoters. EMBO J. 2011;30:3786–3798. doi: 10.1038/emboj.2011.262. PubMed DOI PMC
Epping M.T., Wang L., Edel M.J., Carlée L., Hernandez M., Bernards R. The Human Tumor Antigen PRAME Is a Dominant Repressor of Retinoic Acid Receptor Signaling. Cell. 2005;122:835–847. doi: 10.1016/j.cell.2005.07.003. PubMed DOI
Wang Z., Pascal L.E., Chandran U.R., Chaparala S., Lv S., Ding H., Qi L., Wang Z. ELL2 Is Required for the Growth and Survival of AR-Negative Prostate Cancer Cells. Cancer Manag. Res. 2020;12:4411–4427. doi: 10.2147/CMAR.S248854. PubMed DOI PMC
Zang Y., Pascal L.E., Zhou Y., Qiu X., Wei L., Ai J., Nelson J.B., Zhong M., Xue B., Wang S., et al. ELL2 regulates DNA non-homologous end joining (NHEJ) repair in prostate cancer cells. Cancer Lett. 2018;415:198–207. doi: 10.1016/j.canlet.2017.11.028. PubMed DOI PMC
Ali M., Ajore R., Wihlborg A.K., Niroula A., Swaminathan B., Johnsson E., Stephens O.W., Morgan G., Meissner T., Turesson I., et al. The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression. Nat. Commun. 2018;9:1–9. doi: 10.1038/s41467-018-04082-2. PubMed DOI PMC
Li N., Johnson D.C., Weinhold N., Kimber S., Dobbins S.E., Mitchell J.S., Kinnersley B., Sud A., Law P.J., Orlando G., et al. Genetic Predisposition to Multiple Myeloma at 5q15 Is Mediated by an ELL2 Enhancer Polymorphism. Cell Rep. 2017;20:2556–2564. doi: 10.1016/j.celrep.2017.08.062. PubMed DOI PMC
Georgiadis P., Topinka J., Vlachodimitropoulos D., Stoikidou M., Gioka M., Stephanou G., Autrup H., Demopoulos N.A., Katsouyanni K., Sram R., et al. Interactions between CYP1A1 polymorphisms and exposure to environmental tobacco smoke in the modulation of lymphocyte bulky DNA adducts and chromosomal aberrations. Carcinog. 2004;26:93–101. doi: 10.1093/carcin/bgh294. PubMed DOI
Al-Dayel F., Al-Rasheed M., Ibrahim M., Bu R., Bavi P., Abubaker J., Al-Jomah N., Mohamed G.H., Moorji A., Uddin S., et al. Polymorphisms of drug-metabolizing enzymes CYP1A1, GSTT and GSTP contribute to the development of diffuse large B-cell lymphoma risk in the Saudi Arabian population. Leuk. Lymphoma. 2008;49:122–129. doi: 10.1080/10428190701704605. PubMed DOI
Onnis A., Finetti F., Patrussi L., Gottardo M., Cassioli C., Spanò S., Baldari C.T. The small GTPase Rab29 is a common regulator of immune synapse assembly and ciliogenesis. Cell Death Differ. 2015;22:1687. doi: 10.1038/cdd.2015.17. PubMed DOI PMC
MacLeod D.A., Rhinn H., Kuwahara T., Zolin A., Di Paolo G., McCabe B.D., Marder K.S., Honig L.S., Clark L.N., Small S.A., et al. RAB7L1 Interacts with LRRK2 to Modify Intraneuronal Protein Sorting and Parkinson’s Disease Risk. Neuron. 2013;77:425–439. doi: 10.1016/j.neuron.2012.11.033. PubMed DOI PMC
Tröger J., Moutty M.C., Skroblin P., Klussmann E. A-kinase anchoring proteins as potential drug targets. Br. J. Pharmacol. 2012;166:420–433. doi: 10.1111/j.1476-5381.2011.01796.x. PubMed DOI PMC
Vergarajauregui S., Becker R., Steffen U., Sharkova M., Esser T., Petzold J., Billing F., Kapiloff M.S., Schett G., Thievessen I., et al. AKAP6 orchestrates the nuclear envelope microtubule-organizing center by linking golgi and nucleus via AKAP9. Elife. 2020;9:1–30. doi: 10.7554/eLife.61669. PubMed DOI PMC
Perino A., Ghigo A., Scott J.D., Hirsch E. Anchoring Proteins as Regulators of Signaling Pathways. Circ. Res. 2012;111:482–492. doi: 10.1161/CIRCRESAHA.111.262899. PubMed DOI PMC
Zhou Z., Qiu R., Liu W., Yang T., Li G., Huang W., Teng X., Yang Y., Yu H., Yang Y., et al. BCAS3 exhibits oncogenic properties by promoting CRL4A-mediated ubiquitination of p53 in breast cancer. Cell Prolif. 2021;54:e13088. doi: 10.1111/cpr.13088. PubMed DOI PMC
Bärlund M., Monni O., Weaver J.D., Kauraniemi P., Sauter G., Heiskanen M., Kallioniemi O.-P., Kallioniemi A. Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer†. Genes, Chromosom. Cancer. 2002;35:311–317. doi: 10.1002/gcc.10121. PubMed DOI
Metelli A., Wu B.X., Riesenberg B., Guglietta S., Huck J.D., Mills C., Li A., Rachidi S., Krieg C., Rubinstein M.P., et al. Thrombin Contributes to Cancer Immune Evasion via Proteolysis of Platelet-Bound GARP to Activate LTGF-β. Sci. Transl. Med. 2020;12:4860. doi: 10.1126/scitranslmed.aay4860. PubMed DOI PMC
Hahn S.A., Neuhoff A., Landsberg J., Schupp J., Eberts D., Leukel P., Bros M., Weilbaecher M., Schuppan D., Grabbe S., et al. A key role of GARP in the immune suppressive tumor microenvironment. Oncotarget. 2016;7:42996–43009. doi: 10.18632/oncotarget.9598. PubMed DOI PMC
Jin H., Sun L., Tang L., Yu W., Li H. Expression of GARP Is Increased in Tumor-Infiltrating Regulatory T Cells and Is Correlated to Clinicopathology of Lung Cancer Patients. Front. Immunol. 2017;8:138. doi: 10.3389/fimmu.2017.00138. PubMed DOI PMC
Faget J., Biota C., Bachelot T., Gobert M., Treilleux I., Goutagny N., Durand I., Léon-Goddard S., Blay J.Y., Caux C., et al. Early Detection of Tumor Cells by Innate Immune Cells Leads to Treg Recruitment through CCL22 Production by Tumor Cells. Cancer Res. 2011;71:6143–6152. doi: 10.1158/0008-5472.CAN-11-0573. PubMed DOI
Tsujikawa T., Yaguchi T., Ohmura G., Ohta S., Kobayashi A., Kawamura N., Fujita T., Nakano H., Shimada T., Takahashi T., et al. Autocrine and paracrine loops between cancer cells and macrophages promote lymph node metastasis via CCR4/CCL22 in head and neck squamous cell carcinoma. Int. J. Cancer. 2013;132:2755–2766. doi: 10.1002/ijc.27966. PubMed DOI
Kimura S., Nanbu U., Noguchi H., Harada Y., Kumamoto K., Sasaguri Y., Nakayama T. Macrophage CCL22 expression in the tumor microenvironment and implications for survival in patients with squamous cell carcinoma of the tongue. J. Oral Pathol. Med. 2019;48:677–685. doi: 10.1111/jop.12885. PubMed DOI
Thomas J.K., Mir H., Kapur N., Bae S., Singh S. CC chemokines are differentially expressed in Breast Cancer and are associated with disparity in overall survival. Sci. Rep. 2019;9:1–12. doi: 10.1038/s41598-019-40514-9. PubMed DOI PMC
Nakanishi T., Imaizumi K., Hasegawa Y., Kawabe T., Hashimoto N., Okamoto M., Shimokata K. Expression of macrophage-derived chemokine (MDC)/CCL22 in human lung cancer. Cancer Immunol. Immunother. 2006;55:1320–1329. doi: 10.1007/s00262-006-0133-y. PubMed DOI PMC
Wågsäter D., Dienus O., Löfgren S., Hugander A., Dimberg J. Quantification of the chemokines CCL17 and CCL22 in human colorectal adenocarcinomas. Mol. Med. Rep. 2008;1:211–217. doi: 10.3892/mmr.1.2.211. PubMed DOI