Cancer cell mitochondria: the missing puzzle in predicting response to PD-1/PD-L1 inhibitors

Nahid Nafissi; Farzad Taghizadeh-Hesary

doi:10.1515/oncologie-2025-0420

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Cancer cell mitochondria: the missing puzzle in predicting response to PD-1/PD-L1 inhibitors

Nahid Nafissi und Farzad Taghizadeh-Hesary

Veröffentlicht/Copyright: 19. November 2025

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Aus der Zeitschrift Oncologie Band 27 Heft 6

Abstract

Immunotherapy with anti-programmed cell death protein 1 (PD-1) is a promising anticancer treatment. However, only a minority of patients benefit from anti-PD-1 antibodies. Therefore, identifying the corresponding predictive factors is crucial. Emerging studies have found that the mitochondrial status of immune cells determines tumor response to anti-PD-1 antibodies. Here, we propose a novel hypothesis, based on recent experimental evidence, introducing cancer cell mitochondrial content as a new predictive factor for response to anti-PD-1 immunotherapy. A recent experiment on triple-negative breast cancer cells demonstrated that chemotherapy-induced ATPase family AAA domain–containing protein 3A (ATAD3A) expression levels regulate programmed death ligand-1 (PD-L1) on cancer cells. Accordingly, high ATAD3A expression is associated with high PD-L1 expression, poor tumor response to immunotherapy, and poor overall survival. In contrast, clinical evidence shows that high PD-L1 expression is associated with better response to immunotherapy and improved survival. This discrepancy forms the basis of our hypothesis. We propose that ATAD3A overexpression promotes poor response to anti-PD-1 therapy not by upregulating PD-L1, but by supporting mitochondrial metabolism. ATAD3A is a mitochondrial protein that maintains mitochondrial function and structure under endoplasmic reticulum stress. Therefore, mitochondrial biogenesis may serve as a novel predictive factor for response to anti-PD-(L)1 antibodies.

Keywords: cancer; mitochondria; ATAD3A; immune checkpoint inhibitors; immune resistance

Introduction

Cancer remains a major global health concern [1]. Immune checkpoint inhibitors targeting the programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) axis have transformed cancer therapy. PD-L1 expression on tumor cells – either cancer cells or their surrounding supporting cells in the tumor microenvironment – and its interaction with PD-1 on recruited anti-tumoral immune cells directly impairs immune reactivation [2], 3]. Recent evidence has revealed an additional mechanism by which PD-L1 overexpression on cancer cells indirectly suppresses the anti-tumor immune response. Cheng et al. [4] found that PD-L1 upregulation in triple-negative breast cancer (TNBC) cells can further inhibit immune activity by stimulating the expression of ecto-5′-nucleotidase (NT5E) on cancer cells. NT5E (also known as CD73) inhibits anti-tumor immunity by converting adenosine monophosphate (AMP) into adenosine, a potent immunosuppressor [5].

Clinical evidence indicates that only a minority of patients benefit from PD-1/PD-L1 inhibitors (PDi). A meta-analysis in patients with TNBC reported the overall response rate of just 12 % with anti-PD-L1 monotherapy in the PD-L1–positive population [6]. Current predictive factors, including PD-L1 expression level, tumor mutation burden, T-cell infiltration rate, tumor neoantigen load, and tumor-associated macrophage infiltration, provide valuable insights but do not fully capture the complexity of treatment response [7]. Consequently, there remains a crucial need to identify and validate additional predictive biomarkers to more effectively guide the clinical application of PDi [8].

Emerging evidence highlights immune cells’ mitochondrial biogenesis as a key determinant of response to PDi, with enhanced mitochondrial activation improving treatment outcomes [9], 10]. This commentary introduces a novel perspective: the mitochondrial status of cancer cells themselves may also be a critical factor in shaping tumor response to PDi. To this end, cancer cells actively enhance their mitochondrial content – both in quality and quantity – through multiple mechanisms (outlined in the following sections), thereby promoting PD-L1 expression and improving their resistance to intrinsic anti-tumor immune response on one hand, and enhancing their resistance to PDi on the other hand. The following sections clarify these intricate mechanisms.

Subcellular PD-L1 distribution governed by ATAD3A

Experimental evidence

In an experimental study on TNBC, Xie et al. [11] demonstrated that the ATPase family AAA domain–containing protein 3A (ATAD3A)–PTEN-induced kinase 1 (PINK1)–mitophagy axis regulates the subcellular distribution of PD-L1, which in turn shapes tumor response to chemoimmunotherapy. They classified TNBC into two groups: tumors with mitochondrial PD-L1 accumulation after exposure to paclitaxel (named MITO signature), and tumors with cell membrane PD-L1 accumulation (CM signature). The MITO group exhibited greater infiltration of activated T cells (marked by IFN-γ expression), higher clinical response rates, and improved overall survival, whereas the CM group was characterized by exhausted PD-1–positive T cells, poor treatment response, and poor prognosis. Notably, MITO tumors had low ATAD3A expression, while CM tumors exhibited high ATAD3A expression. Mechanistically, high ATAD3A expression would inhibit PINK1-mediated anchoring of PD-L1 molecules to the mitochondrial membrane, resulting in PD-L1 accumulation on the cell membrane of cancer cells. While this work provides critical mechanistic insight, it does not adhere to the available clinical evidence, as outlined below.

Discrepancy with clinical evidence

Xie et al. concluded that high ATAD3A expression and high cell membrane-bound PD-L1 correlated with poor tumor response to chemoimmunotherapy [11]. This observation contrasts with findings from the phase III KEYNOTE-355 clinical trial on patients with TNBC. In that trial, patients with a combined positive score (CPS) ≥10 demonstrated longer overall survival compared to those with CPS<10 in the chemoimmunotherapy group (23 months vs. 14 months) [12]. This discrepancy suggests that the ATAD3A-PD-L1 axis alone cannot explain the improved prognosis of MITO-signature tumors to PDi, and additional parallel mechanisms may be involved. To better understand these mechanisms, it is helpful to briefly review ATAD3A and its functions in the cell.

ATAD3A as a mitochondrial integrity factor

ATAD3A is an inner mitochondrial membrane AAA+ ATPase that maintains mitochondrial DNA organization, cristae structure, and mitochondria-ER contact sites [13]. These functions preserve mitochondrial metabolism essential for cancer cell survival under endoplasmic stress [14], including endoplasmic stress led by paclitaxel [15]. Using this prelude, we propose an additional perspective of Xie et al.’s finding [11], as follows: in TNBC cells, paclitaxel exposure upregulates ATAD3A as a stress response, protecting mitochondria from damage. Therefore, tumors with high ATAD3A expression not only induce PD-L1 redistribution to the cell membrane but also preserve mitochondrial structures, providing various advantages that support cancer cells’ immune evasion, as outlined in the following section.

Mitochondria are vital for cancer cell immune evasion

Mitochondria: shared assets of cancer and immune cells

Functional mitochondria within cancer cells enhance their immune evasion capacity through several mechanisms: (I) promoting tumor microenvironment acidification via stabilization of hypoxia-inducible factor-1α (HIF-1α) and upregulation of carbonic anhydrase IX (CA-IX) [16], 17]; (II) facilitating competitive glucose uptake in cancer cells through HIF-1 stabilization, thereby limiting glucose availability for immune cell function [17], 18]; (III) suppressing major histocompatibility complex class I (MHC-I)-mediated antigen presentation through activating mitogen-activated protein kinase (MAPK) signaling pathways [19], 20]; (IV) driving T cell exhaustion through PD-L1–PD-1 signaling by impairing mitochondrial fission [21]; and (V) supporting galectin-9 expression and secretion by cancer cells, which activates immune checkpoints via T cell immunoglobulin and mucin domain-containing protein 3 (Tim3) axis [22]. On the other hand, mitochondrial activation in immune cells enhances their proliferation, memory function, cytotoxicity [23], and tumor recognition by downregulating PD-1 expression [24]. Thus, we may conclude that mitochondria are shared requirements for both cancer and immune cells, fueling a competition in which they either facilitate immune evasion or empower immunosurveillance. The following section outlines how cancer cells compete with immune cells over mitochondria.

Mitochondria-enhancing strategies of cancer cells

Cancer cells employ multiple strategies to strengthen their mitochondrial content, some in competing with immune cells (Figure 1). These mechanisms can be categorized into three groups:

Receiving mitochondria from surrounding cells: cancer cells can import mitochondria from the surrounding microenvironment, including tumor-infiltrating neurons [25], neighboring tumor cells [26], and cancer-associated fibroblasts [27];
Improving mitochondrial content over immune cells: In addition, cancer cells can directly hijack functional mitochondria from T cells and NK cells through well-designed tunneling nanotubes [28]. Recent evidence demonstrates that cancer cells can export their own damaged mitochondria, besides mitophagy inhibitors, to impair T cell metabolism [29]. Additional mechanisms include induction of mitochondrial dysfunction in immune cells through PD-1/PD-L1 signaling [30] or by tumor-derived exosomes [31];
Enhancing mitochondrial quality: cancer cells also upregulate mitochondria-enhancing regulators such as peroxisome proliferator–activated receptor gamma coactivator 1-alpha (PGC-1α) and mitofusin to optimize mitochondrial biogenesis and functionality [32], 33].

Figure 1:

Strategies by which cancer cells compete with tumor-infiltrating lymphocytes to enhance their own mitochondrial content while undermining that of immune cells. (A) Cancer cells can acquire mitochondria from surrounding cancer-associated fibroblasts, tumor-infiltrating nerves, and neighboring cancer cells. (B) They further increase their mitochondrial pool by hijacking mitochondria from T cells, (C) while simultaneously impairing T cell function by transferring damaged mitochondria and releasing mitophagy-inhibiting factors. In addition, (D) cancer cells can damage immune cell mitochondria indirectly via exosome secretion or (E) directly through PD-1/PD-L1 interactions. (F) They can also improve the quality of their own mitochondria through the activation of PGC-1α and mitofusin-related pathways.

Therefore, cancer cells pursue various strategies to improve their mitochondrial content both in quality and quantity. This characteristic has been demonstrated in rapidly proliferating cancer cells, which exhibit higher mitochondrial temperatures [34], 35]. This increase in temperature likely supports their rapid growth by enhancing the mitochondrial malate–aspartate shuttle (MAS) and the glycerol 3-phosphate shuttle (G3PS) [36]. When the mitochondrial functional reserve cannot keep pace with the high proliferation rate, backup metabolic pathways are activated, ultimately leading to MAS and G3PS saturation and increased lactate production – a hallmark of the Warburg effect [37].

Conclusions

While evidence shows that ATAD3A expression is a determinant of PD-L1 redistribution, we propose that ATAD3A also contributes to immune resistance by sustaining mitochondrial metabolism and suppressing tumor immunogenicity. Evaluating cancer cell mitochondrial function may therefore complement PD-L1 scoring as a predictive biomarker and guide strategies to improve the efficacy of anti–PD-1 immunotherapy.

Corresponding author: Farzad Taghizadeh-Hesary, MD, Breast Cancer Research Center, Iran University of Medical Sciences, Tehran, 14496-14535, Iran, E-mail: taghizadeh_hesary.f@iums.ac.ir

Research ethics: Not applicable.
Informed consent: Not applicable.
Author contributions: Farzad Taghizadeh-Hesary: Conceptualization, Investigation, Writing- Original draft preparation, Writing- Reviewing and Editing; Nahid Nafissi: Supervision, Writing- Reviewing and Editing.
Use of Large Language Models, AI and Machine Learning Tools: None declared.
Conflict of interest: The authors declare no conflicts of interest to report regarding the present study.
Research funding: The authors received no specific funding for this study.
Data availability: Not applicable.

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Received: 2025-09-26

Accepted: 2025-11-06

Published Online: 2025-11-19

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cancer; mitochondria; ATAD3A; immune checkpoint inhibitors; immune resistance

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