Single-cell differential abundance detection: A new angle on dissecting tumor heterogeneity

Table 1 Some specific applications of differential abundance methods in the study of tumor heterogeneity

Tumor type	Practical application	DA method	Ref.
Head and neck squamous cell carcinoma	Milo identified FRC-like fibroblasts as significantly enriched in immune-hot HNSCC tumors, correlating with better immunotherapy response	Milo	[44]
Gastric cancer	The DA method revealed increasing immune cell abundance (T cell, B cell, NK cell) from non-atrophic gastritis to gastric cancer, with intestinal metaplasia as the key immune evasion turning point	Milo	[34]
Colorectal cancer	DA analysis showed BRAFi + EGFRi enriched EECs in BRAFV600E CRC, while LSD1 inhibition blocked this and enhanced efficacy	propeller	[38]
High-grade serous ovarian cancer	DA analysis revealed myeloid-driven CD8+ T cell exhaustion in ovarian cancer post-chemotherapy, highlighting NECTIN2-TIGIT as an immunotherapy target	propeller	[32]
Pancreatic cancer	DA analysis revealed that neoadjuvant therapy reshapes the pancreatic cancer TME, causing significant shifts in specific immune and fibroblast subpopulations	scCODA	[45]
Lung cancer	Cydar revealed that lung cancers with different driver mutations exhibit significant shifts in T cell subsets, shaping distinct differentiation patterns. Additionally, diffcyt linked specific CAF phenotypes (ifnCAFs, iCAFs) to good prognosis and others (tCAFs, hypoxic tCAFs) to poor prognosis	Cydar/diffcyt	[46,47]
Clear cell renal cell carcinoma	DA analysis showed high-risk ccRCC patients had protumor immune phenotypes lacking specific immune checkpoints	propeller	[48]
Melanoma	The propeller showed immune “cold” uveal melanoma had depleted immune cell subsets, while “hot” cases were enriched with immune response-related cells. Additionally, Milo revealed significant enrichment of antitumor immune cells after personalized neoantigen vaccination in melanoma patients	propeller/Milo	[49,50]
Multiple myeloma	DA-seq showed that post-BCMA CAR-T therapy, responders enriched effector immune cells, while non-responders enriched immunosuppressive subsets. The propeller used DA to compare immune cells in long-term multiple myeloma survivors and controls, finding significant lasting changes decades after treatment	DA-seq/propeller	[51,52]
B cell lymphoma	scCODA showed responders to CAR-T therapy had significant enrichment of antitumor immune cell subsets. Cydar revealed regulatory CAR-T cells enriched in resistant patients after CD19-CAR-T therapy, linked to treatment resistance	scCODA/Cydar	[53,54]
Acute myeloid leukemia	DA analysis revealed significant myeloid and immune cell changes in STAG2-mutant AML, linked to disease and gene abnormalities	Cydar	[55]
Pediatric Hodgkin lymphoma	DA analysis showed multiple T cell subsets were reduced in pediatric Hodgkin lymphoma tumors, indicating widespread T cell suppression	DCATS	[56]

FRC: Fibroblastic reticular cell; HNSCC: Head and neck squamous cell carcinoma; DA: Differential abundance; BRAFi: V-raf murine sarcoma viral oncogene homolog B inhibitor; EGFRi: Epidermal growth factor receptor inhibition; EECs: Enteroendocrine cells; BRAF^V600E: V-raf murine sarcoma viral oncogene homolog B (V600E); CRC: Colorectal cancer; LSD1: Lysine-specific demethylase 1; CD: Cluster of differentiation; NECTIN2: Nectin cell adhesion molecule 2; TIGIT: T-cell immunoglobulin and ITIM domain; TME: Tumor microenvironment; CAF: Cancer-associated fibroblast; ifnCAF: Interferon-responsive-cancer-associated fibroblast; iCAF: Inflammatory cancer-associated fibroblast; tCAF: Tumor-associated fibroblast; ccRCC: Clear cell renal cell carcinoma; BCMA: B-cell maturation antigen; CAR-T: Chimeric antigen receptor T-cell; AML: Acute myeloid leukemia.