Backgroud: Allogeneic haematopoietic stem cell transplantation (allo-HSCT) is a curative treatment for haematological malignancies. Sequential transplantation of haploidentical stem cell and umbilical cord blood (haplo+cord HSCT) among recipients with relapsed/refractory (R/R) leukaemia exhibited superior survival outcomes compared with single cord HSCT. However, the underlying mechanisms remain unclear.

Methods: Here, we profiled and compared single-cell gene expression and chromatin accessibility in bone marrow from 16 patients receiving haplo+cord or single cord HSCT.

Results: We observed distinct compositions and functions of global immune landscapes, with haplo+cord HSCT exhibiting effective anti-tumour and anti-viral immunity mediated by type I interferon signalling. Analysis of T cells revealed specific CD8⁺ T cell subtype (CD8-c1), enriched in recipients with haplo+cord HSCT, which was also confirmed by flow cytometry. Functionally, gene signature scoring suggests a dual effector and memory property of CD8-c1 that potentially offers long-term protection. Furthermore, single-cell multi-omics analysis delineated the expression of cytotoxic-related genes up-regulated in CD8-c1 are cooperatively regulated by enhancer networks. Notably, a proportion-based survival analysis indicated that high proportion of CD8-c1 was associated with better survival.

Conclusion: Our results collectively demonstrate that a population of CD8⁺ T cells with effector and memory properties contributes to improved survival in patients with R/R leukaemia receiving haplo+cord HSCT.

Lysozyme (LYZ) is a naturally occurring antimicrobial protein first discovered in the 1920s. As a key component of innate immunity, its antimicrobial effects and immunomodulatory functions in bacterial defence have been extensively characterized. However, emerging evidence since the 1950s has revealed its complex involvement in tumour progression, with conflicting reports of both tumour-suppressive and tumour-promoting effects across different cancer types. A critical knowledge gap remains in understanding the mechanistic basis for this duality, exacerbated by reliance on single-omics approaches and small cohorts in previous studies. This review focuses on mammalian C-type LYZ (referred to as LYZ hereafter unless specified) and integrates multi-omics data (transcriptomics and proteomics) with clinical and mechanistic research to systematically dissect its dual roles in cancer. By analysing cross-cancer heterogeneity through multi-omics perspectives, we emphasize its dual promise as both a prognostic biomarker and an actionable therapeutic target, aiming to provide new insights for precision oncology.

Background: DNA methylation and chromatin accessibility are pivotal epigenetic regulators of gene expression and cellular identity, with significant implications in tumorigenesis and progression. Current single-cell multi-omics methods are limited in throughput and sensitivity, hindering comprehensive biomarker discovery.

Methods: We developed single-cell split-pool ligation-based multi-omics sequencing technology (SpliCOOL-seq), a high-throughput single-cell sequencing technology that simultaneously profiles whole-genome DNA methylation and chromatin accessibility in thousands of cells. By integrating in situ GpC methylation, universal Tn5 tagmentation, and split-pool combinatorial barcoding, SpliCOOL-seq achieves enhanced sensitivity and scalability.

Results: SpliCOOL-seq accurately distinguished lung cancer cell types based on genetic and multiple epigenetic modalities and revealed that the two DNA methyltransferase (DNMT) inhibitors, 5-Azacitidine and Decitabine, both cause large-scale demethylation but in distinct patterns. Applied to primary lung adenocarcinoma, SpliCOOL-seq identified tumour subclones within the tumour lesion and uncovered novel DNA methylation biomarkers (e.g., FAM124B, SFN, OR7E47P) associated with patient survival. Additionally, we demonstrated accelerated epigenetic ageing and mitotic activity in tumour subclones, providing new insights into tumorigenesis.

Conclusion: SpliCOOL-seq achieves parallel profiling of whole-genome DNA methylation and chromatin accessibility in the same individual cells in a high-throughput manner and is hopefully used to illustrate regulatory interactions under different cell states. SpliCOOL-seq enables high-resolution, multi-modal epigenetic profiling at single-cell resolution, offering a powerful platform for discovering cancer biomarkers. Its application reveals novel therapeutic targets and early-diagnostic markers, underscoring its potential in precision oncology.

The prognostic relevance of HLA class I (HLA-I)-mediated immunity in cancer immunotherapy remains unclear. We introduce deltaHED, a novel metric that quantifies evolutionary divergence between germline and tumour-acquired HLA-I alleles, integrating both inherited and somatic immunogenetic variation. Using whole-exome sequencing, we analysed deltaHED across three independent cohorts: 164 patients with recurrent/metastatic nasopharyngeal carcinoma (RM/NPC) from the POLARIS-02 trial (PD-1 monotherapy), 88 melanoma patients receiving PD-1 monotherapy, and 477 esophageal squamous cell carcinoma (ESCC) patients from the JUPITER-06 trial (PD-1 plus chemotherapy vs. chemotherapy alone). High deltaHED was significantly associated with increased tumour mutational burden and neoantigen load (p < .001), but predicted worse progression-free survival (PFS) and overall survival (OS) in patients receiving PD-1 blockade across all three cancers. In ESCC, this association was observed only in the immunotherapy arm, not in patients treated with chemotherapy alone. High deltaHED also correlated with increased mutations in antigen-processing and T-cell receptor pathways. These findings establish deltaHED as a clinically relevant biomarker of immune divergence with potential to improve patient stratification and guide personalised immunotherapy strategies.

Background: Efferocytosis is a critical physiological process in which phagocytes clear apoptotic cells to maintain tissue homeostasis. However, within the tumour microenvironment (TME), this process is systematically hijacked by tumour cells, transforming it into a key pathological mechanism that drives immunosuppression, tumour progression and therapeutic resistance.

Key findings: This review systematically elucidates the central role of metabolic reprogramming in this functional reversal, emphasising that efferocytosis is essentially an immunometabolic intersection process precisely regulated by metabolism. By releasing various metabolites such as ATP, lactate, adenosine and sphingosine-1-phosphate (S1P), apoptotic tumour cells not only recruit tumour-associated macrophages (TAMs) but also metabolically pre-program their functions, inducing polarisation towards a pro-tumourigenic M2-like phenotype. During the recognition stage, tumour cells exploit metabolic abnormalities, such as glycosylation and lipid oxidation, to modify surface ‘eat-me/don't-eat-me’ signals, thereby hijacking macrophage recognition and engulfment programs. Upon completion of engulfment, systemic reprogramming of amino acid, lipid and glucose metabolism occurs within macrophages. These metabolic alterations synergistically lock their immunosuppressive phenotype and establish a metabolic symbiosis between the tumour and stromal cells.

Conclusions: Based on these mechanisms, this review further explores translational strategies targeting the efferocytic–metabolic axis, aiming to reprogram the immunosuppressive efferocytosis into immune-activating events to overcome TME-mediated immunosuppression and enhance current therapeutic efficacy. By deeply dissecting the metabolic regulatory networks of efferocytosis, we aim to pave new directions for cancer immunotherapy, achieving a paradigm shift from ‘metabolic hijacking’ to ‘metabolic interventional therapy’.

Background: Acute leukaemia is a highly aggressive malignancy with significant unmet therapeutic needs, partly due to epigenetic dysregulation. Here, we uncover deoxynucleotidyl transferase terminal-interacting protein 1 (DNTTIP1) within the mitotic deacetylase complex (MiDAC) as a previously unrecognised epigenetic regulator crucial for leukaemic cell survival and elucidate its mechanistic and translational significance.

Methods: Using cellular, biochemical, and genetic perturbations, coupled with validation in multiple in vivo leukaemia mouse models, we characterised DNTTIP1's role in acute leukaemia. An integrated multi-omics analysis incorporating RNA-seq, cleavage under targets and tagmentation (CUT&Tag) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) revealed that DNTTIP1 recruits histone deacetylase 1/2 (HDAC1/2) to silence BCL2-modifying factor (BMF) and drive leukaemogenesis, validated by chromatin immunoprecipitation quantitative PCR (ChIP-qPCR). Drug synergy assays identify poly(ADP-ribose) polymerase (PARP)/HDAC/BCL2 inhibitor combinatorial efficacy.

Results: DNTTIP1 depletion impaired MiDAC recruitment in acute leukaemia, leading to histone H3 lysine 27 (H3K27) hyperacetylation at the BMF promoter and reactivating this effector. Upregulated BMF disrupted BCL2-mediated survival, triggering coordinated autophagy and apoptosis. Combined HDAC1/2 and BCL2 inhibition exerts synergistic anti-leukaemic effects, a therapeutic strategy currently under clinical evaluation. Further, PARP inhibition profoundly enhanced this synergy by impairing DNA damage repair, unveiling a novel triple-combination strategy.

Conclusions: Our work defines the DNTTIP1‒HDAC1/2‒BMF axis as a pivotal epigenetic vulnerability in acute leukaemia and provides preclinical rationale for targeting this axis. These findings offer a validated biological framework for advancing this targeted combination therapy into clinical trials.

Background: Lymph node (LN) metastasis is a well-established independent prognostic factor in head and neck squamous cell carcinoma (HNSCC). Formation of suppressive tumour immune microenvironment (TIME) is a major contributor to tumour immune evasion and metastasis. However, the TIME landscape underlying LN-metastatic HNSCC remains poorly elucidated.

Methods: A total of 688 866 single-cell transcriptomes across 212 HNSCC samples were integrated. Comprehensive bioinformatic analyses on single-cell RNA sequencing and microarray datasets revealed a TREM2⁺ tumour-associated macrophage (TAM) cluster associated with LN metastasis. The functional role of TREM2⁺ TAMs was investigated through multiplex immunohistochemistry (mIHC) staining in clinical HNSCC cohort and in vitro co-culture experiments. Furthermore, machine learning algorithms were employed to construct a prognostic model for HNSCC.

Results: Integrative single-cell analysis revealed the immunosuppressive TIME of LN-metastatic HNSCC, characterised by high infiltration of exhausted CD8⁺ T cells (CD8⁺ Tex). We identified a specific TREM2⁺ TAM cluster that was strongly associated with CD8⁺ Tex infiltration and LN metastasis. In vitro experiment confirmed that TREM2⁺ TAMs promoted CD8⁺ T cell exhaustion. Mechanistically, TREM2⁺ TAMs exhibited a terminally differentiated phenotype driven by ETV5, and secreted SPP1 to interact with CD44 on CD8⁺ T cells, thus upregulating BHLHE40 to promote CD8⁺ Tex formation. Clinically, a prognostic model based on TREM2⁺ TAM signature genes was trained to independently predict HNSCC outcomes.

Conclusions: This study delineates the mechanism that TREM2⁺ TAMs promote LN metastasis in HNSCC by facilitating CD8⁺ T cells exhaustion via SPP1–CD44–BHLHE40 axis, proposing TREM2⁺ TAMs as potential therapeutic target for HNSCC.

Background: Acute kidney injury (AKI) frequently progresses to chronic kidney disease (CKD), but the underlying mechanisms of this transition remain unclear. While TIMP2 is a known biomarker for AKI, its direct pathogenic role in the AKI-CKD transition has not been fully elucidated.

Methods: TIMP2 expression was evaluated in multiple murine models, including unilateral ischemia-reperfusion injury (UIR), unilateral ureteral obstruction (UUO), and cisplatin-induced nephropathy. To investigate its function, we employed a tubule-specific, inducible TIMP2 knockout mouse model (Ksp-CreERT2; TIMP2fl/fl) and a tubular overexpression model.

Results: TIMP2 was significantly upregulated during the AKI-CKD transition across all tested models. Tubule-specific deletion of TIMP2 markedly attenuated renal fibrosis, suppressed senescence-associated secretory phenotypes (SASP), and promoted tubular repair. Conversely, TIMP2 overexpression exacerbated cellular senescence and fibrotic remodeling. Mechanistically, TIMP2 was found to bind to the Wnt co-receptor LRP6, promoting its phosphorylation and subsequent β-catenin signaling activation, a process independent of its canonical matrix metalloproteinase (MMP) inhibitory function.

Conclusions: TIMP2 is a central mediator of maladaptive repair that links cell senescence and fibrotic reprogramming via the LRP6/β-catenin pathway. These findings suggest that TIMP2 serves not only as a biomarker but also as a potential therapeutic target for mitigating the AKI-CKD transition.

Background: Subarachnoid haemorrhage (SAH), a devastating subtype of stroke, is predominantly caused by the rupture of intracranial aneurysms. Emerging evidence indicates that the risk of intracranial aneurysm rupture correlates with elevated serum levels of fatty acids and pro-inflammatory cytokines. Moreover, increased serum concentrations of adipocyte fatty acid-binding protein (A-FABP), an inflammation-related adipokine, have been associated with poorer prognosis in SAH. However, the precise roles of A-FABP in SAH pathogenesis and its biomarker potential in cerebrospinal fluid (CSF) remain unclear.

Methods: CSF from 40 SAH patients and 30 controls was analysed by targeted fatty acid metabolomics. Experimental SAH mice were induced by endovascular perforation in both genetic deletion and pharmacological inhibition of A-FABP. Brain injury was quantified by neurobehavioural test, inflammatory cytokine expression and TUNEL staining. In vitro, conditioned medium from fatty acid-stimulated microglia was applied to primary neurons to evaluate apoptosis. Microglial metabolic reprogramming was assayed with Seahorse XF assays.

Results: CSF revealed significant metabolic disruption in SAH, characterized by arachidonic acid (AA), linoleic acid and palmitic acid (PA). Enrichment analysis implicated A-FABP plays a crucial role in SAH pathogenesis. Notably, elevated A-FABP levels independently predicted increased SAH severity and poorer prognosis. In mice model of SAH, A-FABP was significantly upregulated in microglia. Genetic deletion and pharmacological inhibition of A-FABP significantly ameliorated brain injury, including neurological deficits, neuroinflammation and neuronal apoptosis. Mechanistically, PA and AA promoted BV2 microglial inflammation via an A-FABP-dependent manner, subsequently inducing apoptosis in co-cultured primary neurons. Moreover, A-FABP inhibition reprogrammed microglial metabolism, enhancing fatty acid β-oxidation and energy supply. Proteomics further identified the JAK2/STAT3 as a downstream pathway of A-FABP-mediated neuroinflammation.

Conclusions: A-FABP is a promising biomarker and translatable therapeutic target to improve SAH outcome. Targeting A-FABP disrupts fatty acids–driven neuroinflammation and microglial metabolic reprogramming to reduce brain injury after SAH.

A central hurdle limiting the success of T-cell-based immunotherapies is the progressive dysfunction of T cells, known as exhaustion. Overcoming this exhausted state is therefore a pivotal objective in translational oncology and immunology. The advent of single-cell multiomics has fundamentally revised the once-prevailing view of exhaustion as a uniform endpoint. Instead, it is now recognised as a dynamic differentiation process comprising a spectrum of distinct cellular states. This spectrum is organised along a hierarchical axis, originating from progenitor-exhausted (Tpex) cells that retain proliferative potential and advancing towards terminally exhausted (Tex) populations with severely impaired effector functions. We undertake a comprehensive synthesis of multiomics data—spanning transcriptomic, epigenomic, metabolomic, proteomic and posttranslational modification (PTM)-proteomic layers—to decipher the interconnected regulatory programmes that dictate commitment along this exhaustion axis. From this integrated analysis, we derive a unified mechanistic framework that delineates the molecular drivers of Tpex cell fate determination and terminal exhaustion. Beyond its explanatory power for basic biology, this framework serves as a direct roadmap for therapeutic innovation, highlighting novel nodes for intervention aimed at reinvigorating the exhausted T-cell compartment. The practical application of these insights holds significant promise for enhancing the efficacy of established current immunotherapeutic platforms.

Background: Skin cancers, including basal cell carcinoma (BCC), squamous cell carcinoma (SCC), cutaneous melanoma (CM) and acral melanoma (AM), exhibit profound heterogeneity in clinical behaviour and therapeutic response. However, how tumour-immune ecosystems are remodelled across skin cancer types and disease stages, and how these changes influence immune escape and treatment resistance, remain poorly understood.

Methods: Here, we integrate single-cell transcriptomics data from 102 skin cancer samples (including adjacent normal skin, early-stage and advanced-stage tumours), with bulk RNA-seq prognosis cohorts, immunofluorescence staining and in vitro assays to define clinically relevant immune remodelling patterns.

Results: Our analyses identify a malignant NARS2⁺NDUFC2⁺ melanoma cell subpopulation, characterised by reduced MHC-I expression, enriched in advanced-stage tumours and associated with worse survival and immunotherapy response. CRISPR screening further showed that NARS2 and NDUFC2 are necessary for the proliferation of melanoma cells, highlighting these genes as potential therapeutic targets. Tumour-associated macrophages (TAMs) originate from both FCN1⁺ monocytes and FOLR2⁺ tissue-resident macrophages, displaying two polarisation states with distinct prognostic associations. Specifically, pro-inflammatory CXCL9⁺CXCL10⁺ TAMs are enriched in SCC, while tissue-remodelling SPP1⁺ TAMs are predominant in melanoma. Immunofluorescence staining confirmed that SPP1⁺ macrophage accumulation correlates with advanced stage, metastasis and poor prognosis in the melanoma cohort. Immune ecotype analysis reveals a transition from ‘T-cell-dominant’ ecotypes to ‘desert’ ecotypes as disease advances in BCC, CM and AM. Cell‒cell communication analysis shows that ‘T-cell-dominant’ ecotypes have higher MHC-I signalling pathways in tumour cells, whereas ‘Desert’ ecotypes have higher SPP1⁺ macrophage signalling, underlining the role of SPP1 on immune remodelling. Functional assays confirm that melanoma cells could drive M2 polarisation and SPP1 upregulation in macrophages. Knocking down or overexpressing SPP1 correspondingly alters M2 gene expression in macrophages.

Conclusions: This study establishes a pan-skin cancer immune remodelling framework, providing a foundation for biomarker discovery and the development of new immunotherapy strategies.