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Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

Bacteria of the genus Streptomyces have complex life cycles involving cellular differentiation and multicellular structures that have never been observed in archaea. Here, the authors show that several halophilic archaea display a life cycle resembling that of Streptomyces bacteria, undergoing cellular differentiation into mycelia and spores.

The reason of mature tertiary lymphoid structures (mTLS) correlates with better prognosis and responses to immune checkpoint blockade (ICB) remains incompletely understood. By employing sequencing and spatial transcriptomics strategies, the authors show that mTLS are enriched with progenitor exhausted CD4⁺ T cells that promotes activation of T and B cells.

Here Tai et al. unveil elevated formation of the C-terminal binding protein (CtBP)–tripartite-motif-containing protein 28 (TRIM28) complex in breast cancer cells and mutual protection between CtBP and TRIM28. This complex is required for mammary gland development and its high levels lead to breast cancer metastasis by repressing autophagy.

Integrating the Pancharatnam–Berry phase with integrated resonant nanoantennas in a metalens design produces an achromatic device capable of full-colour imaging in the visible range in transmission mode.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

A trans-ancestry meta-analysis of GWAS of glycemic traits in up to 281,416 individuals identifies 99 novel loci, of which one quarter was found due to the multi-ancestry approach, which also improves fine-mapping of credible variant sets.

The authors show that ELL3 maintains chromosomal ploidy by promoting spindle assembly and driving chromosome movement in oocytes. Deficiency of ELL3 results in oocyte aneuploidy and may lead to early miscarriage.

The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

Mir-22 has been shown to be an oncogenic microRNA in breast cancer and myelodysplastic syndrome. Here, the authors show that mir-22 functions as a tumour suppressor in de novoacute myeloid leukaemia by inhibiting the expression of several oncogenes and that restoring mir-22 expression suppresses AML progression.

Cell adhesion molecules (CAMs) are key for programming bacterial cell-cell adhesion. By leveraging the transfer of selectable marker genes between bacterial cells, the authors present a method for discovering synthetic CAMs that target naturally occurring bacterial surface components.

A printing technique in which functional particles are directly incorporated into soft polymers using particle engulfment—a process in which particles are spontaneously subsumed by the polymer matrix via surface energy—can be used to create elastic devices with wireless sensing, communication and power transfer capabilities.

Ultrahigh electromechanical response is accomplished by inducing extreme structural instability from competing antiferroelectric and ferroelectric orders.

Resistance to 5-fluorouracil and cisplatin (5FU + CDDP) presents a major issue in patients with gastric cancer. Here, the authors establish 5FU + CDDP resistant intestinal gastric cancer patient-derived organoids and identify JAK/STAT-ADAR1 altered lipid metabolism as a regulator of chemoresistance.

Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

Substantial efforts have been devoted to the construction of axially chiral allenes, however, the strategies to prepare chiral exocyclic allenes are still rare. This work describes a copper-catalyzed asymmetric synthesis of exocyclic allenes by simultaneous control of axial and central chirality.

Mitochondrial dysfunction in cardiomyocytes contributes to the pathogenesis during heart failure. Here the authors report that the transcriptional repressor HEY2 regulates mitochondrial metabolism and cardiac function in adult mouse and zebrafish hearts.

The semileptonic decay channels of the Λc baryon can give important insights into weak interaction, but decay into a neutron, positron and electron neutrino has not been reported so far, due to difficulties in the final products’ identification. Here, the BESIII Collaboration reports its observation in e+e- collision data, exploiting machine-learning-based identification techniques.

How RNA polymerase II subunits enter the nucleus is not well understood. Here, the authors show that Transport and Golgi organization protein 6, TANGO6, recruits RNA polymerase II subunit B2, RPB2, to the ER membrane in a retrograde manner and transports it to the nucleus with the aid of importins.

The authors show that the Salmonella effector SopF is activated by ARF GTPases to ADP-ribosylate a glutamine in the V-ATPase subunit ATP6V0C, blocking xenophagy or other selective autophagy types independent of proton-pumping activity.

Any TFs other than OCT4 that can individually induce the formation of mouse iPSCs are currently lacking. Here, Xiao et.al. report a single-SALL4-mediated somatic reprogramming method and reveal the underlying mechanism of this process.

Genome assemblies for the SunUp transgenic papaya and its progenitor Sunset identify three transgene-insertions in SunUp. Resequencing of 86 papaya genomes highlights the impacts of breeding and geographic origin.

A method leveraging antibodies conjugated with barcoded DNA strands to linearize closely spaced interactions from individual 3D protein complexes allows for the mapping of pairwise and higher-order protein interactions within cells.

Ni et al. report that Snail1 promotes mammary tumour initiation and maintenance independently of its role in EMT. They show that Snail1 forms a complex with HDAC1 and p53 that results in p53 inactivation and degradation, permitting tumour formation.

While Bell inequalities have been violated several times—mostly in photonic systems—their violations within particle physics experiments are less explored. Here, the BESIII Collaboration showcases Bell-violating nonlocal correlations between entangled hyperon pairs.

A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

Electrochemical water splitting is promising for sustainable energy, but relies on development of electrocatalysts for hydrogen evolution. Here the authors report nitrogen- and ruthenium-codoped carbon nanowires in which ruthenium atoms in a carbon matrix drive electrocatalysis of hydrogen evolution

Active cell contraction drives hole nucleation, fracture and crack propagation in a tissue monolayer through a process reminiscent of dewetting thin films.

Observations of optical flares from AT2022tsd (the ‘Tasmanian Devil’) show that they have durations on the timescale of minutes, occur over a period of months, are highly energetic, are probably nonthermal and have supernova luminosities.

Some cancer patients first present with metastases where the location of the primary is unidentified; these are difficult to treat. In this study, using machine learning, the authors develop a method to determine the tissue of origin of a cancer based on whole sequencing data.

Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

The assembly of the Photosystem II proximal antenna CP47 remains a challenging question. Here the authors show that FPB1 and PAM68 act coordinately with Alb3 and the SecY/E translocon to facilitate the co-translational integration of specific regions of CP47 into thylakoids.

Comprehensive analyses of Cas9 proteins shed light on the evolution of the CRISPR–Cas9 system, and identify a pro-CRISPR accessory protein in bacteria that boosts CRISPR-mediated immunity by enhancing the DNA binding and cleavage activity of Cas9.

Cancer stem cells contribute to breast cancer metastasis and recurrence. Here the authors show that TRIB3 enhances breast cancer stemness through interaction with AKT to promote FOXO1 stability, which then increases SOX2 activity.

Urolithin A (UA) is a gut microbiome-derived metabolite that has been therapeutically explored in aging-related diseases and exerts its benefits in part through effects on mitochondria. Here Girotra, Chiang and colleagues show that UA administration boosts mitochondrial recycling in hematopoietic stem cells and reverses aging features in both the hematopoietic and immune systems.

Toxic amyloid-beta plaque and harmful inflammation are two leading hallmarks of Alzheimer’s disease (AD), and precise AD therapy is elusive due to the lack of dual-targeting therapy function, limited blood-brain barrier penetration, and low imaging sensitivity. Here, the authors address these issues by designing a near-infrared-II aggregation-induced emission nanotheranostic for precise AD therapy.

Chemical vapor deposition enables the scalable production of 2D semiconductors, but the grown materials are usually affected by high defect densities. Here, the authors report a hydroxide vapour phase deposition method to synthesize wafer-scale monolayer WS₂ with reduced defect density and electrical properties comparable to those of exfoliated flakes.

Currently, there is limited understanding of the molecular subtypes of fumarate hydratase (FH)-deficient renal cell carcinoma (RCC). Here, the authors employ integrated genomics and transcriptomics to develop a CpG site-specific methylation signature for the identification of FH-deficient RCC, and to identify three distinct molecular subtypes for this rare but highly lethal kidney cancer.

The recent thrust toward flexible nanoscale devices creates a need for two-dimensional piezoelectric materials. Here, the authors find large piezoelectric response in NbOI₂ flakes ranging from 4 nm to the bulk.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

Newly evolved Xanthomonas citri pv. malvacearum isolates triggers recent bacterial blight outbreaks in cotton. Here, the authors show that a recently evolved TALE, Tal7b, activates host susceptibility genes GhSWEET14a and GhSWEET14b rather than GhSWEET10 to confer pathogenicity in these new isolates.