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The spatial organisation of the tumour microenvironment (TME) can affect immune responses that control tumour growth. Here, the authors use single-cell transcriptomics and spatial transcriptomics to identify a lymphocyte aggregated region (LAR) in gastric cancer and compare its cellular and molecular composition with the neighbouring TME.

3D-printed gel microcilia arrays printed by two-photon polymerization and composed of a soft acrylic acid-co-acrylamide hydrogel with a nanometre-scale network structure are shown to respond to low-voltage electrical stimuli within milliseconds, enabling dynamic individual control and non-reciprocal 3D motion.

Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer.

In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.

Using the shear jamming transition within soft composite solids, non-reciprocal mechanics are achieved for the asymmetric spatiotemporal control of soft materials.

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.

Jiang and colleagues identify ETV7 as a transcriptional node that skews CD8⁺ T cell transcriptional profiles toward exhaustion, consequently limiting antiviral and antitumor efficacy, and show that it can be targeted in CAR T cells to enhance efficacy.

Wang and colleagues perform single-cell profiling of human ovarian cancer samples from five anatomic sites, revealing dynamics of the immune microenvironment in malignant ascites and cell subtypes that may play a role in chemotherapy response.

Long-term observations show that a rising fraction of ammonium nitrate in PM_2.5 reduces aerosol acidity, suppressing the heterogeneous conversion from NO₂ to HONO. This weakens its contribution to the HONO source and atmospheric oxidation capacity.

Comprehensive single-cell transcriptomic analysis of 35 human tissues reveals 12 cross-tissue coordinated cellular modules that exhibit intramodule communication and dynamic changes with ageing, and whose organization is perturbed during cancer progression.

In this study, the authors report a potent neutralizing antibody targeting a conserved epitope within RSV pre-F that shows higher antiviral activity against both RSV-A and -B subgroups in vitro and in small animal models than FDA-approved prophylactic agents.

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.

A real-time in situ magnetization reprogramming method for magnetic soft robots enables dynamic shape control, cooperative multi-tool manipulation and expanded actuation abilities.

The kagome lattice is known to host a rich array of correlated phenomena, but thus far the number of examples of truly two dimensional kagome systems are limited. Here, Pan, Xiong, Dai, Zhang, and coauthors present a two-dimensional Mo-Te compound with a kagome superlattice structure, and multiple kagome bands driven correlated states.

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.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

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.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

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.

Tumour-associated neutrophil populations enriched in the myeloid-cell-enriched tumour immune microenvironment subtype are associated with unfavourable prognosis in humans and mice with liver cancer.

Bin Han and colleagues report the draft genome sequence of the grass carp Ctenopharyngodon idellus, a major commercially farmed species of freshwater fish. Analyses of the grass carp genome identify lineage-specific duplications that may have contributed to the adaptation of this species to a vegetarian diet.

Chen, et al identify peritendon CD26 expressing tendon stem/progenitor cells that contribute to tendon healing, as well as Tenascin-C/YAP dependent heterotopic ossification.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

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.

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.

An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

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 characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.

Nasopharyngeal carcinoma is a diverse cancer characterised by a heterogeneous microenvironment. Here, the authors use single cell sequencing to analyse the tumour microenvironment in 10 nasopharyngeal carcinoma tumours and identify different cell types including immune-suppressive T regulatory, tolerogenic dendritic, and exhausted CD8 T cells.

Aging-related intervertebral disc degeneration (IVDD) is a leading cause of lower back pain. Here, the authors perform scRNA-seq analysis of intervertebral disc cells from patients, and identify cell populations and mechanisms associated with IVDD.

MYC oncogene promotes tumourigenesis by coordinating cancer cell proliferation with metabolic adaptation to the consequent excessive oxidative stress. Here, the authors show that nudix hydrolase 1 (NUDT1) is a MYC-driven metabolic vulnerability and generate a NUDT1 protein degrader to treat preclinical MYC-associated cancer.

Single cell RNA-seq is a powerful method to assign cell identity, but the purity of cell clusters arising from this data is not clear. Here the authors present an entropy-based statistic called ROGUE to quantify the purity of cell clusters, and identify subtypes within clusters.

While inhibition of the EZH2 methyltransferase activity has been used for targeting EZH2, its role in cancer progression remains unclear. Here, the authors use neuroblastoma and small cell lung carcinoma model systems and reveal the crosstalk between EZH2 and MYC(N) in the regulation of tumour formation.

The fabrication of n- and p-type semiconducting channels based on the same layered material would simplify the implementation of 2D electronics. Here, the authors report a spatially selective doping method for the synthesis of wafer-scale p- and n-type 2H-MoTe₂ thin films, and their application for the realization of complementary 2D transistor and inverter arrays.

Cheng and colleagues performed an integrative analysis of human colorectal cancer samples to characterize the tumor microenvironment (TME) and stratify patients according to their heterogeneous TMEs, which exploit different immune evasion mechanisms.

Homologous recombination (HR) gene mutations are thought to be synthetic lethal with DNA polymerase theta (Polθ) inhibition. Here, the authors reveal that Polθ addiction is determined by the functional impact of gene mutations on DNA end resection activity.

Finding an efficient way to extract uranium from uranium mine wastewater is an essential environmental requirement. A spontaneous electrochemical method is now shown to enable stable and efficient uranium extraction with net electrical energy output.

Zhang and colleagues analyze single-cell data from patients treated with immunotherapy in five cancer types and find that CXCL13-expressing subsets are implicated in response to treatment in the CD8⁺ and CD4⁺ T cell compartments.

Targeting the specific metabolic phenotypes of colorectal cancer stem cells (CRCSCs) is a potential therapeutic strategy for colorectal cancer (CRC). Here, the authors show that adenylate kinase hCINAP is overexpressed in CRC, binds to the C-terminal domain of LDHA and its depletion inhibits invasion, self-renewal, tumorigenesis and chemoresistance of CRCSCs.