Exploration of Immunology

Table 4. Tumor microenvironment challenges and the proposed solution for each condition.

Challenge	Mechanism	Proposed solution
Regulatory immune cells	Tregs and MDSCs secrete inhibitory cytokines	Depletion via monoclonal antibodies
Soluble immunosuppressive factors	TGF-β, IL-10, and IDO suppress TIL activity	Use inhibitors to neutralize suppressive signals
Hypoxia and metabolic constraints	Hypoxia and glucose deprivation impair TILs	Engineered TILs with hypoxia-resistance pathways
Antigen presentation loss	Own regulation of MHC class I molecules	Epigenetic drugs to restore MHC expression
Physical barriers	Dense ECM limits infiltration	Combine with ECM-degrading enzymes

Return to article view

MDSCs: myeloid-derived suppressor cells; IDO: indoleamine 2,3-dioxygenase; TIL: tumor-infiltrating lymphocyte; MHC: major histocompatibility complex; ECM: extracellular matrix.

Declarations

Acknowledgments

We thank Saveetha University and our respective guides and co-guides for their continued support and feedback during the preparation of this manuscript.

Author contributions

CK: Conceptualization, Methodology, Investigation, Formal analysis, Data curation, Visualization, Writing—original draft. RV: Methodology, Writing—review & editing. AS: Writing—review & editing. VVP: Conceptualization, Supervision, Project administration, Writing—review & editing. All authors read and approved the final manuscript.

Conflicts of interest

The authors declare that they have no competing interests.

Ethical approval

Not applicable.

Consent to participate

Not applicable.

Consent to publication

Not applicable.

Availability of data and materials

All the data discussed is publicly available from cited repositories, such as GEO and TCGA.

Funding

This research received no specific grant from any funding agency, commercial entity, or not-for-profit organization. The authors declare that they did not receive any financial support for the preparation of this article.

Copyright

Publisher’s note

Open Exploration maintains a neutral stance on jurisdictional claims in published institutional affiliations and maps. All opinions expressed in this article are the personal views of the author(s) and do not represent the stance of the editorial team or the publisher.

References

Galon J, Costes A, Sanchez-Cabo F, Kirilovsky A, Mlecnik B, Lagorce-Pagès C, et al. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science. 2006;313:1960–4. [DOI] [PubMed]

Fridman WH, Pagès F, Sautès-Fridman C, Galon J. The immune contexture in human tumours: impact on clinical outcome. Nat Rev Cancer. 2012;12:298–306. [DOI] [PubMed]

Yuan X, Wang J, Huang Y, Shangguan D, Zhang P. Single-Cell Profiling to Explore Immunological Heterogeneity of Tumor Microenvironment in Breast Cancer. Front Immunol. 2021;12:643692. [DOI] [PubMed] [PMC]

Anderson AC, Joller N, Kuchroo VK. Lag-3, Tim-3, and TIGIT: Co-inhibitory Receptors with Specialized Functions in Immune Regulation. Immunity. 2016;44:989–1004. [DOI] [PubMed] [PMC]

Binnewies M, Roberts EW, Kersten K, Chan V, Fearon DF, Merad M, et al. Understanding the tumor immune microenvironment (TIME) for effective therapy. Nat Med. 2018;24:541–50. [DOI] [PubMed] [PMC]

Wherry EJ, Ha S, Kaech SM, Haining WN, Sarkar S, Kalia V, et al. Molecular signature of CD8⁺T cell exhaustion during chronic viral infection. Immunity. 2007;27:670–84. [DOI] [PubMed]

Sen DR, Kaminski J, Barnitz RA, Kurachi M, Gerdemann U, Yates KB, et al. The epigenetic landscape of T cell exhaustion. Science. 2016;354:1165–9. [DOI] [PubMed] [PMC]

Guo X, Zhang Y, Zheng L, Zheng C, Song J, Zhang Q, et al. Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing. Nat Med. 2018;24:978–85. [DOI] [PubMed]

Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, et al. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell. 2018;175:998–1013.e20. [DOI] [PubMed] [PMC]

10.

Li H, van der Leun AM, Yofe I, Lubling Y, Gelbard-Solodkin D, van Akkooi ACJ, et al. Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma. Cell. 2019;176:775–89.e18. [DOI] [PubMed] [PMC]

11.

Kurtulus S, Madi A, Escobar G, Klapholz M, Nyman J, Christian E, et al. Checkpoint Blockade Immunotherapy Induces Dynamic Changes in PD-1^-CD8⁺Tumor-Infiltrating T Cells. Immunity. 2019;50:181–94.e6. [DOI] [PubMed] [PMC]

12.

Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, et al. CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells. Sci Rep. 2017;7:737. [DOI] [PubMed] [PMC]

13.

Schumacher TN, Schreiber RD. Neoantigens in cancer immunotherapy. Science. 2015;348:69–74. [DOI] [PubMed]

14.

Duhen T, Duhen R, Montler R, Moses J, Moudgil T, de Miranda NF, et al. Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors. Nat Commun. 2018;9:2724. [DOI] [PubMed] [PMC]

15.

Wherry EJ, Kurachi M. Molecular and cellular insights into T cell exhaustion. Nat Rev Immunol. 2015;15:486–99. [DOI] [PubMed] [PMC]

16.

Togashi Y, Shitara K, Nishikawa H. Regulatory T cells in cancer immunosuppression—implications for anticancer therapy. Nat Rev Clin Oncol. 2019;16:356–71. [DOI] [PubMed]

17.

Rosenberg SA, Restifo NP, Yang JC, Morgan RA, Dudley ME. Adoptive cell transfer: a clinical path to effective cancer immunotherapy. Nat Rev Cancer. 2008;8:299–308. [DOI] [PubMed] [PMC]

18.

Luo H, Wang W, Mai J, Yin R, Cai X, Li Q. The nexus of dynamic T cell states and immune checkpoint blockade therapy in the periphery and tumor microenvironment. Front Immunol. 2023;14:1267918. [DOI] [PubMed] [PMC]

19.

Dudley ME, Wunderlich JR, Robbins PF, Yang JC, Hwu P, Schwartzentruber DJ, et al. Cancer regression and autoimmunity in patients after clonal repopulation with antitumor lymphocytes. Science. 2002;298:850–4. [DOI] [PubMed] [PMC]

20.

Tumeh PC, Harview CL, Yearley JH, Shintaku IP, Taylor EJM, Robert L, et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature. 2014;515:568–71. [DOI] [PubMed] [PMC]

21.

Ebert PJR, Cheung J, Yang Y, McNamara E, Hong R, Moskalenko M, et al. MAP Kinase Inhibition Promotes T Cell and Anti-tumor Activity in Combination with PD-L1 Checkpoint Blockade. Immunity. 2016;44:609–21. [DOI] [PubMed]

22.

Sade-Feldman M, Jiao YJ, Chen JH, Rooney MS, Barzily-Rokni M, Eliane J, et al. Resistance to checkpoint blockade therapy through inactivation of antigen presentation. Nat Commun. 2017;8:1136. [DOI] [PubMed] [PMC]

23.

Kazemi MH, Sadri M, Najafi A, Rahimi A, Baghernejadan Z, Khorramdelazad H, et al. Tumor-infiltrating lymphocytes for treatment of solid tumors: It takes two to tango? Front Immunol. 2022;13:1018962. [DOI] [PubMed] [PMC]

24.

Li F, Li C, Cai X, Xie Z, Zhou L, Cheng B, et al. The association between CD8+ tumor-infiltrating lymphocytes and the clinical outcome of cancer immunotherapy: A systematic review and meta-analysis. EClinicalMedicine. 2021;41:101134. [DOI] [PubMed] [PMC]

25.

Kinker GS, Greenwald AC, Tal R, Orlova Z, Cuoco MS, McFarland JM, et al. Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity. Nat Genet. 2020;52:1208–18. [DOI] [PubMed] [PMC]

26.

Wu TD, Madireddi S, de Almeida PE, Banchereau R, Chen YJ, Chitre AS, et al. Peripheral T cell expansion predicts tumour infiltration and clinical response. Nature. 2020;579:274–8. [DOI] [PubMed]

27.

Spitzer MH, Nolan GP. Mass Cytometry: Single Cells, Many Features. Cell. 2016;165:780–91. [DOI] [PubMed] [PMC]

28.

Lee J, Ahn E, Kissick HT, Ahmed R. Reinvigorating Exhausted T Cells by Blockade of the PD-1 Pathway. For Immunopathol Dis Therap. 2015;6:7–17. [DOI] [PubMed] [PMC]

29.

Goff SL, Smith FO, Klapper JA, Sherry R, Wunderlich JR, Steinberg SM, et al. Tumor infiltrating lymphocyte therapy for metastatic melanoma: analysis of tumors resected for TIL. J Immunother. 2010;33:840–7. [DOI] [PubMed] [PMC]

30.

Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016;352:189–96. [DOI] [PubMed] [PMC]

31.

Yu Z, Shi J, Fang Y, Zhao Y, Xu A, Li N. Developing innovative strategies of tumor-infiltrating lymphocyte therapy for tumor treatment. Oncol Rep. 2024;51:85. [DOI] [PubMed] [PMC]

32.

Zheng C, Zheng L, Yoo J, Guo H, Zhang Y, Guo X, et al. Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing. Cell. 2017;169:1342–56.e16. [DOI] [PubMed]

33.

Simoni Y, Becht E, Fehlings M, Loh CY, Koo S, Teng KWW, et al. Bystander CD8⁺T cells are abundant and phenotypically distinct in human tumour infiltrates. Nature. 2018;557:575–9. [DOI] [PubMed]

34.

Hartmann FJ, Babdor J, Gherardini PF, Amir ED, Jones K, Sahaf B, et al. Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy. Cell Rep. 2019;28:819–31.e4. [DOI] [PubMed] [PMC]

35.

Moncada R, Barkley D, Wagner F, Chiodin M, Devlin JC, Baron M, et al. Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas. Nat Biotechnol. 2020;38:333–42. [DOI] [PubMed]

36.

Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, et al. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Nat Commun. 2018;9:2419. [DOI] [PubMed] [PMC]

37.

Bendall SC, Simonds EF, Qiu P, Amir ED, Krutzik PO, Finck R, et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science. 2011;332:687–96. [DOI] [PubMed] [PMC]

38.

Sebastian A, Hum NR, McCool JL, Wilson SP, Murugesh DK, Martin KA, et al. Single-cell RNA-Seq reveals changes in immune landscape in post-traumatic osteoarthritis. Front Immunol. 2022;13:938075. [DOI] [PubMed] [PMC]

39.

Li H, Humphreys BD. Single Cell Technologies: Beyond Microfluidics. Kidney360. 2021;2:1196–204. [DOI] [PubMed] [PMC]

40.

Wei SC, Duffy CR, Allison JP. Fundamental Mechanisms of Immune Checkpoint Blockade Therapy. Cancer Discov. 2018;8:1069–86. [DOI] [PubMed]

41.

Toor SM, Sasidharan Nair V, Decock J, Elkord E. Immune checkpoints in the tumor microenvironment. Semin Cancer Biol. 2020;65:1–12. [DOI] [PubMed]

42.

Sadelain M, Rivière I, Riddell S. Therapeutic T cell engineering. Nature. 2017;545:423–31. [DOI] [PubMed] [PMC]

43.

Guedan S, Ruella M, June CH. Emerging Cellular Therapies for Cancer. Annu Rev Immunol. 2019;37:145–71. [DOI] [PubMed] [PMC]

44.

June CH, O’Connor RS, Kawalekar OU, Ghassemi S, Milone MC. CAR T cell immunotherapy for human cancer. Science. 2018;359:1361–5. [DOI] [PubMed]

45.

Pauken KE, Sammons MA, Odorizzi PM, Manne S, Godec J, Khan O, et al. Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Science. 2016;354:1160–5. [DOI] [PubMed] [PMC]

46.

Matous JG, Snook JP, Contreras NA, Ramstead AG, Charley KR, Kolawole EM, et al. Shp-1 regulates the activity of low-affinity T cells specific to endogenous self-antigen during melanoma tumor growth and drives resistance to immune checkpoint inhibition. J Immunother Cancer. 2025;13:e010879. [DOI] [PubMed] [PMC]

47.

Philip M, Fairchild L, Sun L, Horste EL, Camara S, Shakiba M, et al. Chromatin states define tumour-specific T cell dysfunction and reprogramming. Nature. 2017;545:452–6. [DOI] [PubMed] [PMC]

48.

Kaech SM, Cui W. Transcriptional control of effector and memory CD8⁺T cell differentiation. Nat Rev Immunol. 2012;12:749–61. [DOI] [PubMed] [PMC]

49.

Gattinoni L, Lugli E, Ji Y, Pos Z, Paulos CM, Quigley MF, et al. A human memory T cell subset with stem cell-like properties. Nat Med. 2011;17:1290–7. [DOI] [PubMed] [PMC]

50.

Li S, Yao Z, Wang H, Ecker JA, Omotoso MO, Lee J, et al. Ex vivo expansion and hydrogel-mediated in vivo delivery of tissue-resident memory T cells for immunotherapy. Sci Adv. 2024;10:eadm7928. [DOI] [PubMed] [PMC]

51.

Chamberlain CA, Bennett EP, Kverneland AH, Svane IM, Donia M, Met Ö. Highly efficient PD-1-targeted CRISPR-Cas9 for tumor-infiltrating lymphocyte-based adoptive T cell therapy. Mol Ther Oncolytics. 2022;24:417–28. [DOI] [PubMed] [PMC]

52.

Shanmugam G, Rakshit S, Sarkar K. HDAC inhibitors: Targets for tumor therapy, immune modulation and lung diseases. Transl Oncol. 2022;16:101312. [DOI] [PubMed] [PMC]

53.

Tanaka A, Sakaguchi S. Regulatory T cells in cancer immunotherapy. Cell Res. 2017;27:109–18. [DOI] [PubMed] [PMC]

54.

Chaudhry A, Rudra D, Treuting P, Samstein RM, Liang Y, Kas A, et al. CD4⁺regulatory T cells control T_H17 responses in a Stat3-dependent manner. Science. 2009;326:986–91. [DOI] [PubMed] [PMC]

55.

Gabrilovich DI, Nagaraj S. Myeloid-derived suppressor cells as regulators of the immune system. Nat Rev Immunol. 2009;9:162–74. [DOI] [PubMed] [PMC]

56.

Batlle E, Massagué J. Transforming Growth Factor-β Signaling in Immunity and Cancer. Immunity. 2019;50:924–40. [DOI] [PubMed] [PMC]

57.

Platten M, von Knebel Doeberitz N, Oezen I, Wick W, Ochs K. Cancer Immunotherapy by Targeting IDO1/TDO and Their Downstream Effectors. Front Immunol. 2015;5:673. [DOI] [PubMed] [PMC]

58.

Palazon A, Goldrath AW, Nizet V, Johnson RS. HIF transcription factors, inflammation, and immunity. Immunity. 2014;41:518–28. [DOI] [PubMed] [PMC]

59.

Sanomachi T, Katsuya Y, Nakatsura T, Koyama T. Next-Generation CAR-T and TCR-T Cell Therapies for Solid Tumors: Innovations, Challenges, and Global Development Trends. Cancers (Basel). 2025;17:1945. [DOI] [PubMed] [PMC]

60.

Pauken KE, Wherry EJ. Overcoming T cell exhaustion in infection and cancer. Trends Immunol. 2015;36:265–76. [DOI] [PubMed] [PMC]

61.

Garcia-Lora A, Algarra I, Garrido F. MHC class I antigens, immune surveillance, and tumor immune escape. J Cell Physiol. 2003;195:346–55. [DOI] [PubMed]

62.

Seliger B. The link between MHC class I abnormalities of tumors, oncogenes, tumor suppressor genes, and transcription factors. J Immunotoxicol. 2014;11:308–10. [DOI] [PubMed]

63.

Henke E, Nandigama R, Ergün S. Extracellular Matrix in the Tumor Microenvironment and Its Impact on Cancer Therapy. Front Mol Biosci. 2020;6:160. [DOI] [PubMed] [PMC]

64.

Chaudhary B, Elkord E. Regulatory T Cells in the Tumor Microenvironment and Cancer Progression: Role and Therapeutic Targeting. Vaccines (Basel). 2016;4:28. [DOI] [PubMed] [PMC]

65.

Sharma P, Allison JP. Immune checkpoint targeting in cancer therapy: toward combination strategies with curative potential. Cell. 2015;161:205–14. [DOI] [PubMed] [PMC]

66.

Tsai KK, Komanduri KV. Tumor-Infiltrating Lymphocyte Therapy for the Treatment of Metastatic Melanoma. Am J Clin Dermatol. 2025;26:733–45. [DOI] [PubMed] [PMC]

67.

Yarchoan M, Hopkins A, Jaffee EM. Tumor Mutational Burden and Response Rate to PD-1 Inhibition. N Engl J Med. 2017;377:2500–1. [DOI] [PubMed] [PMC]

68.

Dudley ME, Wunderlich JR, Yang JC, Sherry RM, Topalian SL, Restifo NP, et al. Adoptive cell transfer therapy following non-myeloablative but lymphodepleting chemotherapy for the treatment of patients with refractory metastatic melanoma. J Clin Oncol. 2005;23:2346–57. [DOI] [PubMed] [PMC]

69.

Goff SL, Dudley ME, Citrin DE, Somerville RP, Wunderlich JR, Danforth DN, et al. Randomized, Prospective Evaluation Comparing Intensity of Lymphodepletion Before Adoptive Transfer of Tumor-Infiltrating Lymphocytes for Patients With Metastatic Melanoma. J Clin Oncol. 2016;34:2389–97. [DOI] [PubMed] [PMC]

70.

Rosenberg SA, Restifo NP. Adoptive cell transfer as personalized immunotherapy for human cancer. Science. 2015;348:62–8. [DOI] [PubMed] [PMC]

71.

Chueh AC, Tse JWT, Tögel L, Mariadason JM. Mechanisms of Histone Deacetylase Inhibitor-Regulated Gene Expression in Cancer Cells. Antioxid Redox Signal. 2015;23:66–84. [DOI] [PubMed] [PMC]

72.

Kwong MLM, Yang JC. Lifileucel: FDA-approved T-cell therapy for melanoma. Oncologist. 2024;29:648–50. [DOI] [PubMed] [PMC]

73.

Wu CY, Rupp LJ, Roybal KT, Lim WA. Synthetic biology approaches to engineer T cells. Curr Opin Immunol. 2015;35:123–30. [DOI] [PubMed] [PMC]

74.

Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S, et al. Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial. Nature. 2019;565:234–9. [DOI] [PubMed] [PMC]

75.

Gros A, Parkhurst MR, Tran E, Pasetto A, Robbins PF, Ilyas S, et al. Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients. Nat Med. 2016;22:433–8. [DOI] [PubMed] [PMC]

76.

Wang Z, Sun P, Li Z, Xiao S. Clinical Advances and Future Directions of Oncolytic Virotherapy for Head and Neck Cancer. Cancers (Basel). 2023;15:5291. [DOI] [PubMed] [PMC]

77.

Ribas A, Hamid O, Daud A, Hodi FS, Wolchok JD, Kefford R, et al. Association of Pembrolizumab With Tumor Response and Survival Among Patients With Advanced Melanoma. JAMA. 2016;315:1600–9. [DOI] [PubMed]

78.

Jain RK. Normalizing tumor microenvironment to treat cancer: bench to bedside to biomarkers. J Clin Oncol. 2013;31:2205–18. [DOI] [PubMed] [PMC]

79.

Doedens AL, Phan AT, Stradner MH, Fujimoto JK, Nguyen JV, Yang E, et al. Hypoxia-inducible factors enhance the effector responses of CD8(+) T cells to persistent antigen. Nat Immunol. 2013;14:1173–82. [DOI] [PubMed] [PMC]

80.

Ganeeva I, Zmievskaya E, Valiullina A, Kudriaeva A, Miftakhova R, Rybalov A, et al. Recent Advances in the Development of Bioreactors for Manufacturing of Adoptive Cell Immunotherapies. Bioeng (Basel). 2022;9:808. [DOI] [PubMed] [PMC]

81.

Perez C, Gruber I, Arber C. Off-the-Shelf Allogeneic T Cell Therapies for Cancer: Opportunities and Challenges Using Naturally Occurring “Universal” Donor T Cells. Front Immunol. 2020;11:583716. [DOI] [PubMed] [PMC]

82.

Cristescu R, Mogg R, Ayers M, Albright A, Murphy E, Yearley J, et al. Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy. Science. 2018;362:eaar3593. [DOI] [PubMed] [PMC]

83.

Valkiers S, de Vrij N, Gielis S, Verbandt S, Ogunjimi B, Laukens K, et al. Recent advances in T-cell receptor repertoire analysis: Bridging the gap with multimodal single-cell RNA sequencing. ImmunoInformatics. 2022;5:100009. [DOI]