Onco-Circuit Addiction and Onco-Nutrient mTORC1 Signaling Vulnerability in a Model of Aggressive T Cell Malignancy.

How genetic lesions drive cell transformation and whether they can be circumvented without compromising function of non-transformed cells are enduring questions in oncology. Here we show that in mature T cells-in which physiologic clonal proliferation is a cardinal feature- constitutive MYC transcription and Tsc1 loss in mice modeled aggressive human malignancy by reinforcing each other's oncogenic programs. This cooperation was supported by MYC-induced large neutral amino acid transporter chaperone SLC3A2 and dietary leucine, which in synergy with Tsc1 deletion overstimulated mTORC1 to promote mitochondrial fitness and MYC protein overexpression in a positive feedback circuit. A low leucine diet was therapeutic even in late-stage disease but did not hinder T cell immunity to infectious challenge, nor impede T cell transformation driven by constitutive nutrient mTORC1 signaling via Depdc5 loss. Thus, mTORC1 signaling hypersensitivity to leucine as an onco-nutrient enables an onco-circuit, decoupling pathologic from physiologic utilization of nutrient acquisition pathways.

Multilayered Immunity by Tissue-Resident Lymphocytes in Cancer.

Lymphocytes spanning the entire innate-adaptive spectrum can stably reside in tissues and constitute an integral component of the local defense network against immunological challenges. In tight interactions with the epithelium and endothelium, tissue-resident lymphocytes sense antigens and alarmins elicited by infectious microbes and abiotic stresses at barrier sites and mount effector responses to restore tissue homeostasis. Of note, such a host cell-directed immune defense system has been recently demonstrated to surveil epithelial cell transformation and carcinoma development, as well as cancer cell metastasis at selected distant organs, and thus represents a primordial cancer immune defense module. Here we review how distinct lineages of tissue-resident innate lymphoid cells, innate-like T cells, and adaptive T cells participate in a form of multilayered cancer immunity in murine models and patients, and how their convergent effector programs may be targeted through both shared and private regulatory pathways for cancer immunotherapy.

Deep generative model deciphers derailed trajectories in acute myeloid leukemia.

Single-cell genomics has the potential to map cell states and their dynamics in an unbiased way in response to perturbations like disease. However, elucidating the cell-state transitions from healthy to disease requires analyzing data from perturbed samples jointly with unperturbed reference samples. Existing methods for integrating and jointly visualizing single-cell datasets from distinct contexts tend to remove key biological differences or do not correctly harmonize shared mechanisms. We present Decipher, a model that combines variational autoencoders with deep exponential families to reconstruct derailed trajectories (https://github.com/azizilab/decipher). Decipher jointly represents normal and perturbed single-cell RNA-seq datasets, revealing shared and disrupted dynamics. It further introduces a novel approach to visualize data, without the need for methods such as UMAP or TSNE. We demonstrate Decipher on data from acute myeloid leukemia patient bone marrow specimens, showing that it successfully characterizes the divergence from normal hematopoiesis and identifies transcriptional programs that become disrupted in each patient when they acquire NPM1 driver mutations.

Speech, Facial and Fine Motor Features for Conversation-Based Remote Assessment and Monitoring of Parkinson's Disease.

We present a cloud-based multimodal dialogue platform for the remote assessment and monitoring of speech, facial and fine motor function in Parkinson's Disease (PD) at scale, along with a preliminary investigation of the efficacy of the various metrics automatically extracted by the platform. 22 healthy controls and 38 people with Parkinson's Disease (pPD) were instructed to complete four interactive sessions, spaced a week apart, on the platform. Each session involved a battery of tasks designed to elicit speech, facial movements and finger movements. We find that speech, facial kinematic and finger movement dexterity metrics show statistically significant differences between controls and pPD. We further investigate the sensitivity, specificity, reliability and generalisability of these metrics. Our results offer encouraging evidence for the utility of automatically-extracted audiovisual analytics in remote mon-itoring of PD and other movement disorders.

Cytotoxic granzyme C-expressing ILC1s contribute to antitumor immunity and neonatal autoimmunity.

Innate lymphocytes are integral components of the cellular immune system that can coordinate host defense against a multitude of challenges and trigger immunopathology when dysregulated. Natural killer (NK) cells and innate lymphoid cells (ILCs) are innate immune effectors postulated to functionally mirror conventional cytotoxic T lymphocytes and helper T cells, respectively. Here, we showed that the cytolytic molecule granzyme C was expressed in cells with the phenotype of type 1 ILCs (ILC1s) in mouse liver and salivary gland. Cell fate-mapping and transfer studies revealed that granzyme C-expressing innate lymphocytes could be derived from ILC progenitors and did not interconvert with NK cells, ILC2s, or ILC3s. Granzyme C defined a maturation state of ILC1s. These granzyme C-expressing ILC1s required the transcription factors T-bet and, to a lesser extent, Eomes and support from transforming growth factor-ß (TGF-ß) signaling for their maintenance in the salivary gland. In a transgenic mouse breast cancer model, depleting ILC1s caused accelerated tumor growth. ILC1s gained granzyme C expression following interleukin-15 (IL-15) stimulation, which enabled perforin-mediated cytotoxicity. Constitutive activation of STAT5, a transcription factor regulated by IL-15, in granzyme C-expressing ILC1s triggered lethal perforin-dependent autoimmunity in neonatal mice. Thus, granzyme C marks a cytotoxic effector state of ILC1s, broadening their function beyond "helper-like" lymphocytes.

Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma.

Immune checkpoint therapy with anti-CTLA-4 and anti-PD-1/PD-L1 has revolutionized the treatment of many solid tumors. However, the clinical efficacy of immune checkpoint therapy is limited to a subset of patients with specific tumor types1,2. Multiple clinical trials with combinatorial immune checkpoint strategies are ongoing; however, the mechanistic rationale for tumor-specific targeting of immune checkpoints is elusive. To garner an insight into tumor-specific immunomodulatory targets, we analyzed 94 patients representing five different cancer types, including those that respond relatively well to immune checkpoint therapy and those that do not, such as glioblastoma multiforme, prostate cancer and colorectal cancer. Through mass cytometry and single-cell RNA sequencing, we identified a unique population of CD73hi macrophages in glioblastoma multiforme that persists after anti-PD-1 treatment. To test if targeting CD73 would be important for a successful combination strategy in glioblastoma multiforme, we performed reverse translational studies using CD73-/- mice. We found that the absence of CD73 improved survival in a murine model of glioblastoma multiforme treated with anti-CTLA-4 and anti-PD-1. Our data identified CD73 as a specific immunotherapeutic target to improve antitumor immune responses to immune checkpoint therapy in glioblastoma multiforme and demonstrate that comprehensive human and reverse translational studies can be used for rational design of combinatorial immune checkpoint strategies.

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment.

Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We profiled 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph nodes, using single-cell RNA-seq. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. Despite significant similarity between normal and tumor tissue-resident immune cells, we observed continuous phenotypic expansions specific to the tumor microenvironment. Analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data from 27,000 additional T cells revealed the combinatorial impact of TCR utilization on phenotypic diversity. Our results support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer. Our results have important implications for characterizing tumor-infiltrating immune cells.

PD-1 Blockade Expands Intratumoral Memory T Cells.

Tumor responses to programmed cell death protein 1 (PD-1) blockade therapy are mediated by T cells, which we characterized in 102 tumor biopsies obtained from 53 patients treated with pembrolizumab, an antibody to PD-1. Biopsies were dissociated, and single-cell infiltrates were analyzed by multicolor flow cytometry using two computational approaches to resolve the leukocyte phenotypes at the single-cell level. There was a statistically significant increase in the frequency of T cells in patients who responded to therapy. The frequency of intratumoral B cells and monocytic myeloid-derived suppressor cells significantly increased in patients' biopsies taken on treatment. The percentage of cells with a regulatory T-cell phenotype, monocytes, and natural killer cells did not change while on PD-1 blockade therapy. CD8(+) memory T cells were the most prominent phenotype that expanded intratumorally on therapy. However, the frequency of CD4(+) effector memory T cells significantly decreased on treatment, whereas CD4(+) effector T cells significantly increased in nonresponding tumors on therapy. In peripheral blood, an unusual population of blood cells expressing CD56 was detected in two patients with regressing melanoma. In conclusion, PD-1 blockade increases the frequency of T cells, B cells, and myeloid-derived suppressor cells in tumors, with the CD8(+) effector memory T-cell subset being the major T-cell phenotype expanded in patients with a response to therapy.

Synthesis and characterisation of halide, separated ion pair, and hydride cyclopentadienyl iron bis(diphenylphosphino)ethane derivatives.

Treatment of anhydrous FeX2 (X = Cl, Br, I) with one equivalent of bis(diphenylphosphino)ethane (dppe) in refluxing THF afforded analytically pure white (X = Cl), light green (X = Br), and yellow (X = I) [FeX2(dppe)]n (X = Cl, ; Br, ; I, ). Complexes are excellent synthons from which to prepare a range of cyclopentadienyl derivatives. Specifically, treatment of with alkali metal salts of C5H5 (Cp, series ), C5Me5 (Cp*, series ), C5H4SiMe3 (Cp', series ), C5H3(SiMe3)2 (Cp'', series ), and C5H3(Bu(t))2 (Cp(tt), series ) afforded [Fe(Cp(†))(Cl)(dppe)] , [Fe(Cp(†))(Br)(dppe)] , and [Fe(Cp(†))(I)(dppe)] (Cp(†) = Cp, Cp*, Cp', Cp'', or Cp(tt)). Dissolution of in acetonitrile, or treatment of with Me3SiI in acetonitrile (no halide exchange reactions were observed in other solvents) afforded the separated ion pair complexes [Fe(Cp(†))(NCMe)(dppe)][I] . Attempts to reduce , , and with a variety of reductants (Li-Cs, KC8, Na/Hg) were unsuccessful. Treatment of with LiAlH4 gave the hydride derivatives [Fe(Cp(†))(H)(dppe)] . This report provides a systematic account of reliable methods of preparing these complexes which may find utility in molecular wire and metal-metal bond chemistries. The complexes reported herein have been characterised by X-ray diffraction, NMR, IR, UV/Vis, and Mössbauer spectroscopies, cyclic voltammetry, density functional theory calculations, and elemental analyses, which have enabled us to elucidate the electronic structure of the complexes and probe the variation of iron redox properties as a function of varying the cyclopentadienyl or halide ligand.

The nature of unsupported uranium-ruthenium bonds: a combined experimental and theoretical study.

Four new uranium-ruthenium complexes, [(Tren(TMS))URu(η(5)-C(5)H(5))(CO)(2)] (9), [(Tren(DMSB))URu(η(5)-C(5)H(5))(CO)(2)] (10), [(Ts(Tolyl))(THF)URu(η(5)-C(5)H(5))(CO)(2)] (11), and [(Ts(Xylyl))(THF)URu(η(5)-C(5)H(5))(CO)(2)] (12) [Tren(TMS)=N(CH(2)CH(2)NSiMe(3))(3); Tren(DMSB)=N(CH(2)CH(2)NSiMe(2)tBu)(3)]; Ts(Tolyl)=HC(SiMe(2)NC(6)H(4)-4-Me)(3); Ts(Xylyl)=HC(SiMe(2)NC(6)H(3)-3,5-Me(2))(3)], were prepared by a salt-elimination strategy. Structural, spectroscopic, and computational analyses of 9-12 shows: i) the formation of unsupported uranium-ruthenium bonds with no isocarbonyl linkages in the solid state; ii) ruthenium-carbonyl backbonding in the [Ru(η(5)-C(5)H(5))(CO)(2)](-) ions that is tempered by polarization of charge within the ruthenium fragments towards uranium; iii) closed-shell uranium-ruthenium interactions that can be classified as predominantly ionic with little covalent character. Comparison of the calculated U-Ru bond interaction energies (BIEs) of 9-12 with the BIE of [(η(5)-C(5)H(5))(3)URu(η(5)-C(5)H(5))(CO)(2)], for which an experimentally determined U-Ru bond disruption enthalpy (BDE) has been reported, suggests BDEs of approximately 150 kJ mol(-1) for 9-12.

A global baseline for spawning aggregations of reef fishes.

Species that periodically and predictably congregate on land or in the sea can be extremely vulnerable to overexploitation. Many coral reef fishes form spawning aggregations that are increasingly the target of fishing. Although serious declines are well known for a few species, the extent of this behavior among fishes and the impacts of aggregation fishing are not appreciated widely. To profile aggregating species globally, establish a baseline for future work, and strengthen the case for protection, we (as members of the Society for the Conservation of Reef Fish Aggregations) developed a global database on the occurrence, history, and management of spawning aggregations. We complemented the database with information from interviews with over 300 fishers in Asia and the western Pacific. Sixty-seven species, mainly commercial, in 9 families aggregate to spawn in the 29 countries or territories considered in the database. Ninety percent of aggregation records were from reef pass channels, promontories, and outer reef-slope drop-offs. Multispecies aggregation sites were common, and spawning seasons of most species typically lasted <3 months. The best-documented species in the database, the Nassau grouper (Epinephelus striatus), has undergone substantial declines in aggregations throughout its range and is now considered threatened. Our findings have important conservation and management implications for aggregating species given that exploitation pressures on them are increasing, there is little effective management, and 79% of those aggregations sufficiently well documented were reported to be in decline. Nonetheless, a few success stories demonstrate the benefits of aggregation management. A major shift in perspective on spawning aggregations of reef fish, from being seen as opportunities for exploitation to acknowledging them as important life-history phenomena in need of management, is urgently needed.

Trace metals and organochlorines in the bamboo shark Chiloscyllium plagiosum from the southern waters of Hong Kong, China.

The bamboo shark Chiloscyllium plagiosum is an abundant benthic species along the shallow continental shelf of Southeast Asia. It is commonly taken by fishermen in China, India, Taiwan and Thailand for human consumption. This study measured trace metal and organochlorine concentrations in C. plagiosum collected from the southern waters of Hong Kong, China. Metals (Ag, Cd, Cr, Cu, Mn, Ni, Pb and Zn) were measured in three different tissues: dorsal muscle, spleen and liver. Polychlorinated biphenyls (PCBs) and chlorinated pesticides in the dorsal muscle were identified and quantified using gas chromatography. Metal concentrations varied among the three different tissues, with liver having higher levels of Ag and Cd, and spleen possessing higher levels of Cu and Mn. Both Ni and Pb in all tissues were below the detection limit. Tissue concentrations of Cr, Cu, Mn and Zn generally decreased with increasing body weight whilst no significant concentration-size relationship was found for other metals. In muscle tissues, total PCBs ranged from 1.056-4.771 ng/g (wet wt.) with a median of 1.801 ng/g, while total DDTs ranged from 0.602-23.55 ng/g with a median of 1.109 ng/g, in which p,p'-DDE was the predominant metabolite. Levels of total hexachlorohexanes and cyclodienes were low. The pesticide p,p'-DDT was the only compound found to be positively correlated with body weight, indicating temporal bioaccumulation of this compound. Zn concentrations in the muscle of C. plagiosum were comparatively higher than recorded in other shark species, however, concentrations of other metals and organochlorines were relatively low. C. plagiosum feeds primarily on polychaetes, shrimps and small fishes, and thus is unlikely to contain levels of contaminants of human health concern.

Resurvey of a reef flat in American Samoa after 85 years reveals devastation to a soft coral (Alcyonacea) community.

One of the earliest quantitative surveys of soft corals, on a reef flat in Pago Pago Harbour, American Samoa, was repeated 85 years later. The alcyoniid communities there, which were the dominant benthic organisms during the initial survey, have suffered a drastic decline of 99% cover in the interim. The most likely causes of the decline are anthropogenic disturbance associated with reclamation along the harbour from the 1940s to early 1960s, compounded by chronic pollution from industrial wastewater discharge from the mid-1950s to late 1980s. The decline in one dominant species, Sinularia polydactyla, is likely to have serious consequences for the reef as unusually for a soft coral, this had been the major reef building species. Life-history traits of certain Sinularia and Sarcophyton, such as slow growth and low rates of sexual reproduction, mean they will be slower to recover from severe disturbance than many scleractinian corals.