Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients

Intra-tumor heterogeneity (ITH) of human tumors is important for tumor progression, treatment response, and drug resistance. However, the spatial distribution of ITH remains incompletely understood. Here, we present spatial analysis of ITH in lung adenocarcinomas from 147 patients using multi-region mass spectrometry of >5,000 regions, single-cell copy number sequencing of ~2,000 single cells, and cyclic immunofluorescence of >10 million cells. We identified two distinct spatial patterns among tumors, termed clustered and random geographic diversification (GD). These patterns were observed in the same samples using both proteomic and genomic data. The random proteomic GD pattern, which is characterized by decreased cell adhesion and lower levels of tumor-interacting endothelial cells, was significantly associated with increased risk of recurrence or death in two independent patient cohorts. Our study presents comprehensive spatial mapping of ITH in lung adenocarcinoma and provides insights into the mechanisms and clinical consequences of GD.

The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution

Cutaneous melanoma is a highly immunogenic malignancy that is surgically curable at early stages but life-threatening when metastatic. Here we integrate high-plex imaging, 3D high-resolution microscopy, and spatially resolved microregion transcriptomics to study immune evasion and immunoediting in primary melanoma. We find that recurrent cellular neighborhoods involving tumor, immune, and stromal cells change significantly along a progression axis involving precursor states, melanoma in situ, and invasive tumor. Hallmarks of immunosuppression are already detectable in precursor regions. When tumors become locally invasive, a consolidated and spatially restricted suppressive environment forms along the tumor-stromal boundary. This environment is established by cytokine gradients that promote expression of MHC-II and IDO1, and by PD1-PDL1-mediated cell contacts involving macrophages, dendritic cells, and T cells. A few millimeters away, cytotoxic T cells synapse with melanoma cells in fields of tumor regression. Thus, invasion and immunoediting can coexist within a few millimeters of each other in a single specimen.

SIGNIFICANCE

The reorganization of the tumor ecosystem in primary melanoma is an excellent setting in which to study immunoediting and immune evasion. Guided by classic histopathology, spatial profiling of proteins and mRNA reveals recurrent morphologic and molecular features of tumor evolution that involve localized paracrine cytokine signaling and direct cell-cell contact. This article is highlighted in the In This Issue feature, p. 1397.

Stepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment

Establishing causal relationships between genetic alterations of human cancers and specific phenotypes of malignancy remains a challenge. We sequentially introduced mutations into healthy human melanocytes in up to five genes spanning six commonly disrupted melanoma pathways, forming nine genetically distinct cellular models of melanoma. We connected mutant melanocyte genotypes to malignant cell expression programs in vitro and in vivo, replicative immortality, malignancy, rapid tumor growth, pigmentation, metastasis, and histopathology. Mutations in malignant cells also affected tumor microenvironment composition and cell states. Our melanoma models shared genotype-associated expression programs with patient melanomas, and a deep learning model showed that these models partially recapitulated genotype-associated histopathological features as well. Thus, a progressive series of genome-edited human cancer models can causally connect genotypes carrying multiple mutations to phenotype.

MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.

Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation

The mechanisms regulating exhaustion of tumor-infiltrating lymphocytes (TIL) and responsiveness to PD-1 blockade remain partly unknown. In human ovarian cancer, we show that tumor-specific CD8+ TIL accumulate in tumor islets, where they engage antigen and upregulate PD-1, which restrains their functions. Intraepithelial PD-1+CD8+ TIL can be, however, polyfunctional. PD-1+ TIL indeed exhibit a continuum of exhaustion states, with variable levels of CD28 costimulation, which is provided by antigen-presenting cells (APC) in intraepithelial tumor myeloid niches. CD28 costimulation is associated with improved effector fitness of exhausted CD8+ TIL and is required for their activation upon PD-1 blockade, which also requires tumor myeloid APC. Exhausted TIL lacking proper CD28 costimulation in situ fail to respond to PD-1 blockade, and their response may be rescued by local CTLA-4 blockade and tumor APC stimulation via CD40L.

Abstract 2747: Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer

Immune checkpoint blockade has emerged as a new therapeutic approach for multiple cancers. The majority of high-grade serous ovarian, fallopian tube or peritoneal cancers (HGSCs) are deficient in homologous recombination (HR) DNA repair, typically due to mutations or hypermethylation of BRCA1 or BRCA2 genes. A detailed understanding how tumor genotypes affect the tumor microenvironment is unknown.

We performed single-cell spatial analysis of the tumor microenvironment using a highly multiplex tissue cyclic immunofluorescence (t-CycIF) platform with a clinically annotated cohort of 31 patients with BRCA1/2 mutated (BRCAmut) tumors, and 13 patients with tumors without alterations in HR genes (HRwt) (Strickland et al, 2016). Using image analysis, we generated single-cell data for 24 markers in over 105 cells. We clustered the cells into tumor, immune, and stromal cells, and further divided the tumor cells into 7 metaclusters, immune cells into 10 subtypes and stromal cells into 9 metaclusters based on their functional states.

Overall, the BRCAmut tumors showed a higher proportion of tumor cells over stromal cells as compared to HRwt tumors (p=0.031). Moreover, we found distinct functional states of tumor cell metaclusters with opposing prognostic roles in the tumor HR-genotypes. In immune profiling, the BRCAmut tumors exhibited an increased proportion of overall macrophages as compared to HRwt tumors (p=0.024). By contrast, HRwt tumors exhibited more CD11c expressing antigen-presenting cells than BRCAmut tumors (p=0.0013). Interestingly, the tumors with high CD163 expressing, M2 macrophages exhibited a lower overall immune diversity (Simpson's diversity index) in both BRCAmut tumors (p=8.9 × 10−6) and HRwt tumors (p=0.0076). However, the BRCAmut tumors with high immune diversity also had higher proportions of CD11c expressing macrophages (p=0.029). In survival analyses, CD4+ effector T-cells associated with a prolonged platinum free interval exclusively in the BRCAmut tumors (p=0.0011, HR 0.26, 95% CI 0.10-0.66).

In correlative analyses of the tumor-immune-stromal populations, tumor metaclusters associated with distinct immune phenotypes in the BRCAmut tumors. By contrast, immune composition was shaped more by stromal metaclusters in HRwt tumors. These findings further support the differential regulation of tumor microenvironment composition in the tumor HR-genotypes. Further, our preliminary analyses on spatial arrangement of the single-cell subpopulations confirm the distinct microenvironment niches in BRCA1/2 vs HRwt HGSCs.

In conclusion, our single-cell spatial t-CycIF analyses suggest functionally and spatially distinct microenvironments in BRCAmut tumors with the potential to accelerate the development of immunotherapeutic strategies to ultimately improve the treatment and outcomes of patients with ovarian cancer.

Citation Format: Inga-Maria P. Launonen, Nuppu Lyytikäinen, Julia Casado, Ella A. Anttila, Connor A. Jacobson, Jia R. Lin, Zoltan Maliga, Sandro Santaga, Kevin M. Elias, Alan D. D'Andrea, Panagiotis A. Konstantinopoulos, Peter K. Sorger, Anniina Färkkilä. Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2747.

Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity

Obesity is a major cancer risk factor, but how differences in systemic metabolism change the tumor microenvironment (TME) and impact anti-tumor immunity is not understood. Here, we demonstrate that high-fat diet (HFD)-induced obesity impairs CD8⁺ T cell function in the murine TME, accelerating tumor growth. We generate a single-cell resolution atlas of cellular metabolism in the TME, detailing how it changes with diet-induced obesity. We find that tumor and CD8⁺ T cells display distinct metabolic adaptations to obesity. Tumor cells increase fat uptake with HFD, whereas tumor-infiltrating CD8⁺ T cells do not. These differential adaptations lead to altered fatty acid partitioning in HFD tumors, impairing CD8⁺ T cell infiltration and function. Blocking metabolic reprogramming by tumor cells in obese mice improves anti-tumor immunity. Analysis of human cancers reveals similar transcriptional changes in CD8⁺ T cell markers, suggesting interventions that exploit metabolism to improve cancer immunotherapy.

Vascular Disease and Thrombosis in SARS-CoV-2-Infected Rhesus Macaques

The COVID-19 pandemic has led to extensive morbidity and mortality throughout the world. Clinical features that drive SARS-CoV-2 pathogenesis in humans include inflammation and thrombosis, but the mechanistic details underlying these processes remain to be determined. In this study, we demonstrate endothelial disruption and vascular thrombosis in histopathologic sections of lungs from both humans and rhesus macaques infected with SARS-CoV-2. To define key molecular pathways associated with SARS-CoV-2 pathogenesis in macaques, we performed transcriptomic analyses of bronchoalveolar lavage and peripheral blood and proteomic analyses of serum. We observed macrophage infiltrates in lung and upregulation of macrophage, complement, platelet activation, thrombosis, and proinflammatory markers, including C-reactive protein, MX1, IL-6, IL-1, IL-8, TNFα, and NF-κB. These results suggest a model in which critical interactions between inflammatory and thrombosis pathways lead to SARS-CoV-2-induced vascular disease. Our findings suggest potential therapeutic targets for COVID-19.

Author Correction: Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer

Combined PARP and immune checkpoint inhibition has yielded encouraging results in ovarian cancer, but predictive biomarkers are lacking. We performed immunogenomic profiling and highly multiplexed single-cell imaging on tumor samples from patients enrolled in a Phase I/II trial of niraparib and pembrolizumab in ovarian cancer (NCT02657889). We identify two determinants of response; mutational signature 3 reflecting defective homologous recombination DNA repair, and positive immune score as a surrogate of interferon-primed exhausted CD8 + T-cells in the tumor microenvironment. Presence of one or both features associates with an improved outcome while concurrent absence yields no responses. Single-cell spatial analysis reveals prominent interactions of exhausted CD8 + T-cells and PD-L1 + macrophages and PD-L1 + tumor cells as mechanistic determinants of response. Furthermore, spatial analysis of two extreme responders shows differential clustering of exhausted CD8 + T-cells with PD-L1 + macrophages in the first, and exhausted CD8 + T-cells with cancer cells harboring genomic PD-L1 and PD-L2 amplification in the second.

Development of highly selective SH3 binding peptides for Crk and CRKL which disrupt Crk-complexes with DOCK180, SoS and C3G

Many Src Homology 3 (SH3) domains function as molecular adhesives in intracellular signal transduction. Based on previous ultrastructural studies, short motifs which bind to the first SH3 domains of the adapters Crk and CRKL were selectively mutagenised to generate Crk/CRKL SH3-binding peptides of very high affinity and selectivity. Affinities were increased up to 20-fold compared to the best wildtype sequences, while the selectivity against a similar SH3 domain [Grb2SH3(N)] was not only retained, but sometimes increased. Blot techniques with GST-fusion peptides and in solution precipitation assays with biotinylated high affinity Crk binding peptides (HACBPs) were subsequently used to analyse the binding of these sequences to a large panel of SH3 domain-containing fusion proteins. Only those proteins which contained the CrkSH3(1) or CRKLSH3(1) domains bound efficiently to the HACBPs. A GST-HACBP fusion protein precipitated Crk and CRKL proteins out of 35S-labelled and unlabelled cell lysates. Very little binding of other cellular proteins to HACBP was detectable, indicative of a great preference for Crk and CRKL when compared to the wide variety of other endogenous cellular proteins. Moreover, HACBP disrupted in vitro preexisting Crk-complexes with DOCK180 and the exchange factors SoS and C3G, which are known targets of Crk adapters, in a concentration dependent manner. HACBP-based molecules should therefore be useful as highly selective inhibitors of intracellular signalling processes involving Crk and CRKL.

The effects of noise in transient EOAE newborn hearing screening

The use of transient evoked otoacoustic emissions (TEOAEs) has been advocated as the first stage entry level technique for universal newborn hearing screening. To date, the majority of TEOAE infant testing has been conducted under controlled noise conditions; i.e., acoustically treated sound suites. As a result, previously reported TEOAE evaluations may not realistically represent test outcomes in actual hospital screening settings. The purpose of this study was to compare the results of TEOAEs with auditory brainstem response (ABR) hearing screening in a hospital environment where noise conditions do not meet the same ambient noise specifications as those found in sound rooms. A total of 119 stable newborns (67 high risk, 52 normal) ranging in post-conceptual age (PCA) from 33 to 41 weeks received both the ABR and TEOAE screening protocols. Testing was conducted at crib side in either the well baby nursery or the neonatal special care unit (NSCU). Newborn ABR screening failed 8 (3.8%) of 224 ears, whereas TEOAE testing failed 85 (38.4%) and could not test another 22 (9.8%) ears. That is, only 117 (52.2%) of the 224 ears passed the TEOAE test. Using the ABR as the reference test the specificity and sensitivity for TEOAE was 52% and 50%, respectively. Noise levels measured by the probe microphone within the ear canal exceeded those levels (30 dBA SPL) recommended for TEOAE newborn hearing screening. Results of this study suggest that under realistic hearing screening test conditions, TEOAE results may be influenced by the level of noise in the testing environment. Whereas significant advances have been attained in TEOAE measurement during the past decade, clinical evidence supports the need for continued research aimed at solving problems before this technique can be used efficiently for newborn screening.

Follow-up services in newborn hearing screening programs

Newborn hearing screening programs have gained wide acceptance as a means of identifying infants at risk for hearing loss. For the most part, the auditory brainstem response (ABR) technique has been the measurement tool universally adopted in the evaluation of high-risk infants. Over the years, the ABR has been used successfully with a negligible false-negative rate. Unfortunately, program follow-up services have not received similar attention, and there is a lack in program development. This article describes a series of follow-up measures that include the use of a questionnaire sent to the parents/caregivers of 401 infants who pass either the initial or retest ABR screen. A total of 262 (65%) response questionnaires were returned. The results of the questionnaire and recommendations regarding follow-up services are discussed.

Automated and conventional ABR screening techniques in high-risk infants

Test validity is determined by the proportion of results that are diagnostically confirmed and predicted on the measures used to identify the disease process. This article summarizes the results of a series of 224 stable high-risk infants who were screened by automated (ALGO-1) and conventional (Bio-logics LT) ABR instrumentation. Failure criteria was defined as the absence or prolongation of a replicable wave V response (conventional) or Refer by the automated system. The overall failure rates at a 35 dB screening level were comparable between devices. Sensitivity and specificity measures for the ALGO-1 unit were 100 and 96 percent, respectively. Permanent hearing loss was demonstrated in 5 percent of the newborns screened in this study. Advantages of the automated system include a dual artifact rejection system, attenuating ear couplers, and a battery operated design. These findings suggest that the automated ABR screener is a viable alternative to conventional ABR instrumentation for the limited purpose of neonatal auditory screening.

Hearing loss in prison inmates

The incidence of hearing disorders in 34 State Penitentiary prison inmates all with a previous history of drug abuse were investigated. Subjects were evaluated using routine pure-tone air conduction audiometry, immittance measures, and short-latency auditory brain stem responses. Of the 34 inmates, 20 (58.8%) demonstrated normal bilateral peripheral hearing sensitivity, whereas 10 (29.4%) inmates presented with some degree of hearing impairment. In addition, the conflicting results of elevated pure-tone thresholds with normal immittance measures and normal ABR findings suggested that four (11.8%) subjects exhibited functional hearing loss. The results of this study support the reported high incidence of hearing loss in the prison population. The synergistic effects of drug abuse, noise exposure, and head trauma as possible contributing factors are discussed.