Cancer Res Treat.  2025 Apr;57(2):580-589. 10.4143/crt.2024.689.

Higher Microbial Abundance and Diversity in Bronchus-Associated Lymphoid Tissue Lymphomas Than in Non-cancerous Lung Tissues

• Kim JH
• Kim JS
• Choi N
• Koh J
• Jeon YK
• Chang JH
• Hwang ES
• Kim IH

• KMID: 2566874
• DOI: http://doi.org/10.4143/crt.2024.689

Abstract

Purpose
It is well known that the majority of the extranodal marginal zone lymphomas of mucosa-associated lymphoid tissues (MALT lymphomas) are associated with microbiota, e.g., gastric MALT lymphoma with Helicobacter pylori. In general, they are very sensitive to low-dose radiotherapy and chemotherapeutic agents. The microbiota profile is not clearly elucidated in bronchus-associated lymphoid tissue (BALT) lymphoma, a rare type of MALT lymphoma in the lung. Thus, this study aimed to clarify the intratumor microbiome in BALT lymphoma using the third-generation next-generation sequencing (NGS) method.
Materials and Methods
DNAs were extracted from 12 formalin-fixed paraffin-embedded (FFPE) tumor tissues obtained from BALT lymphoma patients diagnosed between 1990 and 2016. 16S rRNA gene was amplified by polymerase chain reaction. Amplicons were sequenced using a Nanopore platform. Next-generation sequencing analysis was performed to assess microbial profiles. For comparison, FFPE specimens from nine non-cancerous lung tissues were also analyzed.
Results
Specific bacterial families including Burkholderiaceae, Bacillaceae, and Microbacteriaceae were associated with BALT lymphoma by a linear discriminant analysis effect size approach. Although the number of specimens was limited, BALT lymphomas exhibited significantly higher microbial abundance and diversity with distinct microbial composition patterns and correlation networks than non-cancerous lung tissues.
Conclusion
This study provides the first insight into intratumor microbiome in BALT lymphoma using the third-generation NGS method. A distinct microbial composition suggests the presence of a unique tumor microenvironment of BALT lymphoma.

Keyword

Bronchus-associated lymphoid tissue (BALT) lymphoma; Extranodal marginal zone B-cell lymphoma; Mucosa-associated lymphoid tissue; Non-Hodgkin lymphoma; Intratumor microbiome

Figure

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  Fig. 1. Phylogenetic and microbial community diversity profiles of samples obtained from patients with bronchus-associated lymphoid tissue (BALT) lymphomas and non-cancerous lung tissues. (A) Actual abundance. (B) Relative abundance. (C) Beta-diversity. (D) Alpha-diversity of each sample. (E) Alpha-diversity of groups.

• 

  Fig. 2. (A) Heat tree analysis of bronchus-associated lymphoid tissue (BALT) lymphomas and non-cancerous lung tissues. (B) Linear discriminant analysis (LDA) of effect size. (C) Correlation network analysis. Nodes (taxa) are interconnected when there is a statistically significant correlation between them. The size of each node reflects the number of its connections, while the thickness of a connection denotes the strength of that correlation.

Reference

References

1. Jaffe ES. The 2008 WHO classification of lymphomas: implications for clinical practice and translational research. Hematology Am Soc Hematol Educ Program. 2009; 523–31.

2. Khalil MO, Morton LM, Devesa SS, Check DP, Curtis RE, Weisenburger DD, et al. Incidence of marginal zone lymphoma in the United States, 2001-2009 with a focus on primary anatomic site. Br J Haematol. 2014; 165:67–77.

3. Ishikawa E, Nakamura M, Satou A, Shimada K, Nakamura S. Mucosa-associated lymphoid tissue (MALT) lymphoma in the gastrointestinal tract in the modern era. Cancers (Basel). 2022; 14:446.

4. Wotherspoon AC, Doglioni C, Diss TC, Pan L, Moschini A, de Boni M, et al. Regression of primary low-grade B-cell gastric lymphoma of mucosa-associated lymphoid tissue type after eradication of Helicobacter pylori. Lancet. 1993; 342:575–7.

5. Xu WS, Chan AC, Lee JM, Liang RH, Ho FC, Srivastava G. Epstein-Barr virus infection and its gene expression in gastric lymphoma of mucosa-associated lymphoid tissue. J Med Virol. 1998; 56:342–50.

6. Lin PH, Kitaguchi Y, Mupas-Uy J, Takahashi Y, Kakizaki H. Bilateral orbital marginal zone B-cell lymphoma of the mucosa-associated lymphoid tissue in a patient with hepatitis B virus infection. Am J Ophthalmol Case Rep. 2017; 7:27–30.

7. Boulanger E, Meignin V, Baia M, Molinier-Frenkel V, Leroy K, Oksenhendler E, et al. Mucosa-associated lymphoid tissue lymphoma in patients with human immunodeficiency virus infection. Br J Haematol. 2008; 140:470–4.

8. Cadranel J, Wislez M, Antoine M. Primary pulmonary lymphoma. Eur Respir J. 2002; 20:750–62.

9. Fiche M, Caprons F, Berger F, Galateau F, Cordier JF, Loire R, et al. Primary pulmonary non-Hodgkin’s lymphomas. Histopathology. 1995; 26:529–37.

10. Adam P, Czapiewski P, Colak S, Kosmidis P, Tousseyn T, Sagaert X, et al. Prevalence of Achromobacter xylosoxidans in pulmonary mucosa-associated lymphoid tissue lymphoma in different regions of Europe. Br J Haematol. 2014; 164:804–10.

11. Chanudet E, Adam P, Nicholson AG, Wotherspoon AC, Ranaldi R, Goteri G, et al. Chlamydiae and Mycoplasma infections in pulmonary MALT lymphoma. Br J Cancer. 2007; 97:949–51.

12. Chong J, Liu P, Zhou G, Xia J. Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nat Protoc. 2020; 15:799–821.

13. Andermann T, Antonelli A, Barrett RL, Silvestro D. Estimating alpha, beta, and gamma diversity through deep learning. Front Plant Sci. 2022; 13:839407.

14. Cha T, Kim HH, Keum J, Kwak MJ, Park JY, Hoh JK, et al. Gut microbiome profiling of neonates using Nanopore MinION and Illumina MiSeq sequencing. Front Microbiol. 2023; 14:1148466.

15. Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol. 2021; 39:1348–65.

16. Cullin N, Azevedo Antunes C, Straussman R, Stein-Thoeringer CK, Elinav E. Microbiome and cancer. Cancer Cell. 2021; 39:1317–41.

17. Wang MB, Liu IY, Gornbein JA, Nguyen CT. HPV-positive oropharyngeal carcinoma: a systematic review of treatment and prognosis. Otolaryngol Neck Surg. 2015; 153:758–69.

18. Marrelli D, Pedrazzani C, Berardi A, Corso G, Neri A, Garosi L, et al. Negative Helicobacter pylori status is associated with poor prognosis in patients with gastric cancer. Cancer. 2009; 115:2071–80.

19. Liu J, Liu C, Yue J. Radiotherapy and the gut microbiome: facts and fiction. Radiat Oncol. 2021; 16:9.

20. Dutta D, Lim SH. Bidirectional interaction between intestinal microbiome and cancer: opportunities for therapeutic interventions. Biomark Res. 2020; 8:31.

21. van Ooij C. Bacterial toxins: Escherichia coli damages host DNA. Nat Rev Microbiol. 2010; 8:534.

22. Coenye T. The family Burkholderiaceae. In : Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The Prokaryotes: Alphaproteobacteria and Betaproteobacteria. Springer;2014. p. 759–76.

23. Mahenthiralingam E, Urban TA, Goldberg JB. The multifarious, multireplicon Burkholderia cepacia complex. Nat Rev Microbiol. 2005; 3:144–56.

24. Leitao JH, Sousa SA, Ferreira AS, Ramos CG, Silva IN, Moreira LM. Pathogenicity, virulence factors, and strategies to fight against Burkholderia cepacia complex pathogens and related species. Appl Microbiol Biotechnol. 2010; 87:31–40.

25. Sousa SA, Soares-Castro P, Seixas AMM, Feliciano JR, Balugas B, Barreto C, et al. New insights into the immunoproteome of B. cenocepacia J2315 using serum samples from cystic fibrosis patients. N Biotechnol. 2020; 54:62–70.

26. Adam P, Gernert C, Schmitt S, Haralambieva E, Ott G, Muller-Hermelink HK, et al. The spectrum of microbiological agents causing pulmonary MALT-type lymphomas: a 16S rRNA-based analysis of microbial diversity. Pathologe. 2008; 29 Suppl 2:290–6.

27. Stackebrandt E. The family Thermoanaerobacteraceae. In : Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. The prokaryotes: Firmicutes and Tenericutes. Springer;2014. p. 413–9.

28. Rabkin CS, Galaid EI, Hollis DG, Weaver RE, Dees SB, Kai A, et al. Thermophilic bacteria: a new cause of human disease. J Clin Microbiol. 1985; 21:553–7.

29. Merlos A, Rodriguez P, Barcena-Uribarri I, Winterhalter M, Benz R, Vinuesa T, et al. Toxins secreted by Bacillus isolated from lung adenocarcinomas favor the penetration of toxic substances. Front Microbiol. 2015; 6:1301.

30. Li N, Zhou H, Holden VK, Deepak J, Dhilipkannah P, Todd NW, et al. Streptococcus pneumoniae promotes lung cancer development and progression. iScience. 2023; 26:105923.

31. Najafi S, Abedini F, Azimzadeh Jamalkandi S, Shariati P, Ahmadi A, Gholami Fesharaki M. The composition of lung microbiome in lung cancer: a systematic review and meta-analysis. BMC Microbiol. 2021; 21:315.

32. Perez-Cobas AE, Ginevra C, Rusniok C, Jarraud S, Buchrieser C. The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia. Cell Rep Med. 2023; 4:101167.

33. Nolan TJ, Gadsby NJ, Hellyer TP, Templeton KE, McMullan R, McKenna JP, et al. Low-pathogenicity Mycoplasma spp. alter human monocyte and macrophage function and are highly prevalent among patients with ventilator-acquired pneumonia. Thorax. 2016; 71:594–600.

34. Perez Vidakovics ML, Riesbeck K. Virulence mechanisms of Moraxella in the pathogenesis of infection. Curr Opin Infect Dis. 2009; 22:279–85.

35. Klima CL, Holman DB, Cook SR, Conrad CC, Ralston BJ, Allan N, et al. Multidrug resistance in Pasteurellaceae associated with bovine respiratory disease mortalities in North America from 2011 to 2016. Front Microbiol. 2020; 11:606438.

36. Kielstein P, Wuthe H, Angen O, Mutters R, Ahrens P. Phenotypic and genetic characterization of NAD-dependent Pasteurellaceae from the respiratory tract of pigs and their possible pathogenetic importance. Vet Microbiol. 2001; 81:243–55.

37. Li KJ, Chen ZL, Huang Y, Zhang R, Luan XQ, Lei TT, et al. Dysbiosis of lower respiratory tract microbiome are associated with inflammation and microbial function variety. Respir Res. 2019; 20:272.

38. Paudel KR, Dharwal V, Patel VK, Galvao I, Wadhwa R, Malyla V, et al. Role of lung microbiome in innate immune response associated with dhronic lung diseases. Front Med (Lausanne). 2020; 7:554.

39. Ferreri AJ, Guidoboni M, Ponzoni M, De Conciliis C, Dell’Oro S, Fleischhauer K, et al. Evidence for an association between Chlamydia psittaci and ocular adnexal lymphomas. J Natl Cancer Inst. 2004; 96:586–94.

40. Chanudet E, Zhou Y, Bacon CM, Wotherspoon AC, Muller-Hermelink HK, Adam P, et al. Chlamydia psittaci is variably associated with ocular adnexal MALT lymphoma in different geographical regions. J Pathol. 2006; 209:344–51.

41. Yamashiro Y, Shimizu T, Oguchi S, Shioya T, Nagata S, Ohtsuka Y. The estimated incidence of cystic fibrosis in Japan. J Pediatr Gastroenterol Nutr. 1997; 24:544–7.

42. Kim JS, Kim IH, Byun JM, Chang JH. Population-based study on the association between autoimmune disease and lymphoma: National Health Insurance Service-National Sample Cohort 2002-2015 in Korea. J Autoimmun. 2021; 121:102647.