Multi-resolution deep learning characterizes tertiary lymphoid structures and their prognostic relevance in solid tumors

BACKGROUND

Tertiary lymphoid structures (TLSs) are dense accumulations of lymphocytes in inflamed peripheral tissues, including cancer, and are associated with improved survival and response to immunotherapy in various solid tumors. Histological TLS quantification has been proposed as a novel predictive and prognostic biomarker, but lack of standardized methods of TLS characterization hampers assessment of TLS densities across different patients, diseases, and clinical centers.

METHODS

We introduce an approach based on HookNet-TLS, a multi-resolution deep learning model, for automated and unbiased TLS quantification and identification of germinal centers in routine hematoxylin and eosin stained digital pathology slides. We developed HookNet-TLS using n = 1019 manually annotated TCGA slides from clear cell renal cell carcinoma, muscle-invasive bladder cancer, and lung squamous cell carcinoma.

RESULTS

Here we show that HookNet-TLS automates TLS quantification across multiple cancer types achieving human-level performance and demonstrates prognostic associations similar to visual assessment.

CONCLUSIONS

HookNet-TLS has the potential to be used as a tool for objective quantification of TLS in routine H&E digital pathology slides. We make HookNet-TLS publicly available to promote its use in research.

Molecular, Immunological, and Clinical Features Associated With Lymphoid Neogenesis in Muscle Invasive Bladder Cancer

Lymphoid neogenesis gives rise to tertiary lymphoid structures (TLS) in the periphery of multiple cancer types including muscle invasive bladder cancer (MIBC) where it has positive prognostic and predictive associations. Here, we explored molecular, clinical, and histological data of The Cancer Genome Atlas, as well as the IMvigor210 dataset to study factors associated with TLS development and function in the tumor microenvironment (TME) of MIBC. We also analyzed tumor immune composition including TLS in an independent, retrospective MIBC cohort. We found that the combination of TLS density and tumor mutational burden provides a novel independent prognostic biomarker in MIBC. Gene expression profiles obtained from intratumoral regions that rarely contain TLS in MIBC showed poor correlation with the prognostic TLS density measured in tumor periphery. Tumors with high TLS density showed increased gene signatures as well as infiltration of activated lymphocytes. Intratumoral B-cell and CD8⁺ T-cell co-infiltration was frequent in TLS-high samples, and such regions harbored the highest proportion of PD-1⁺TCF1⁺ progenitor-like T cells, naïve T cells, and activated B cells when compared to regions predominantly infiltrated by either B cells or CD8⁺ T cells alone. We found four TLS maturation subtypes; however, differences in TLS composition appeared to be dictated by the TME and not by the TLS maturation status. Finally, we identified one downregulated and three upregulated non-immune cell-related genes in TME with high TLS density, which may represent candidates for tumor-intrinsic regulation of lymphoid neogenesis. Our study provides novel insights into TLS-associated gene expression and immune contexture of MIBC and indicates towards the relevance of B-cell and CD8⁺ T-cell interactions in anti-tumor immunity within and outside TLS.

Human CtIP: A 'double agent' in DNA repair and tumorigenesis

Human CtIP was originally identified as an interactor of the retinoblastoma protein and BRCA1, two bona fide tumour suppressors frequently mutated in cancer. CtIP is renowned for its role in the resection of DNA double-strand breaks (DSBs) during homologous recombination, a largely error-free DNA repair pathway crucial in maintaining genome integrity. However, CtIP-dependent DNA end resection is equally accountable for alternative end-joining, a mutagenic DSB repair mechanism implicated in oncogenic chromosomal translocations. In addition, CtIP contributes to transcriptional regulation of G1/S transition, DNA damage checkpoint signalling, and replication fork protection pathways. In this review, we present a perspective on the current state of knowledge regarding the tumour-suppressive and oncogenic properties of CtIP and provide an overview of their relevance for cancer development, progression, and therapy.

Evidence for cluster shape effects on the kinetic energy spectrum in thermionic emission

Experimental kinetic energy release distributions obtained for the thermionic emission from C(n) (-) clusters, 10< or =n< or =20, exhibit significant non-Boltzmann variations. Using phase space theory, these different features are analyzed and interpreted as the consequence of contrasting shapes in the daughter clusters; linear and nonlinear isomers have clearly distinct signatures. These results provide a novel indirect structural probe for atomic clusters associated with their thermionic emission spectra.

Intramolecular recognition in a jet-cooled short peptide chain: γ-turn helicity probed by a neighbouring residue

gamma-Turn, the shortest secondary structure of peptides, exists as two helical forms gamma(l) and gamma(d) of opposite handedness. The present gas phase study of capped l-Phe-Xxx peptides (Xxx = l-Ala, d-Ala or Aib: aminoisobutyric acid) provides a unique example of intramolecular chiral recognition of the gamma-turn helicity on Ala or Aib by the neighbouring residue Phe within the chain. With the chiral l- or d-Ala residues, the presence of a side-chain operates a discrimination between the two helical forms: one of them is widely favoured over the other (gamma(l) or gamma(d), respectively). This enables us to validate and calibrate the recognition capabilities of the nearby l-Phe residue. The discriminating interactions have been precisely characterized from their spectroscopic UV and IR signatures and identified by comparison with quantum chemistry calculations. Then, in the case of the non-chiral residue Aib, the two helical forms of the gamma-turn, which are simultaneously observed in the jet, have been discriminated and assigned by comparison with the chiral residues. The relative abundances of the diastereomeric forms l-Phe-Aib(gamma(l)) and l-Phe-Aib(gamma(d)) enable us to determine the most efficient recognition configuration.