Intratumoral heterogeneity is a critical frontier in understanding how the tumor microenvironment (TME) propels malignant progression. Here, we deconvolute the human pancreatic TME through large-scale integration of histology-guided regional multiOMICs with clinical data and patient-derived preclinical models. We discover "subTMEs," histologically definable tissue states anchored in fibroblast plasticity, with regional relationships to tumor immunity, subtypes, differentiation, and treatment response. "Reactive" subTMEs rich in complex but functionally coordinated fibroblast communities were immune hot and inhabited by aggressive tumor cell phenotypes. The matrix-rich "deserted" subTMEs harbored fewer activated fibroblasts and tumor-suppressive features yet were markedly chemoprotective and enriched upon chemotherapy. SubTMEs originated in fibroblast differentiation trajectories, and transitory states were notable both in single-cell transcriptomics and in situ. The intratumoral co-occurrence of subTMEs produced patient-specific phenotypic and computationally predictable heterogeneity tightly linked to malignant biology. Therefore, heterogeneity within the plentiful, notorious pancreatic TME is not random but marks fundamental tissue organizational units.

Comment in Nat Cell Biol. 2021 Dec;23(12):1221-1223.

Comment on Cell. 2021 Oct 28;184(22):5622-5634.e25.

The scientific and clinical communities have both experienced several harsh lessons on clinical care management and drug development during the COVID-19 pandemic. Here, we discuss several key lessons learned and describe a framework within which our two communities can work together and invest in to improve future pandemic responses.

Comment in Nat Methods. 2021 Dec;18(12):1451.

Comment in Nat Rev Gastroenterol Hepatol. 2021 Dec;18(12):831. Nat Rev Cancer. 2022 Jan;22(1):1. Mol Cell. 2021 Dec 2;81(23):4768-4770.

Mammals use glabrous (hairless) skin of their hands and feet to navigate and manipulate their environment. Cortical maps of the body surface across species contain disproportionately large numbers of neurons dedicated to glabrous skin sensation, in part reflecting a higher density of mechanoreceptors that innervate these skin regions. Here, we find that disproportionate representation of glabrous skin emerges over postnatal development at the first synapse between peripheral mechanoreceptors and their central targets in the brainstem. Mechanoreceptor synapses undergo developmental refinement that depends on proximity of their terminals to glabrous skin, such that those innervating glabrous skin make synaptic connections that expand their central representation. In mice incapable of sensing gentle touch, mechanoreceptors innervating glabrous skin still make more powerful synapses in the brainstem. We propose that the skin region a mechanoreceptor innervates controls the developmental refinement of its central synapses to shape the representation of touch in the brain.

Comment in Nat Rev Neurosci. 2021 Dec;22(12):719. Cell. 2021 Oct 28;184(22):5501-5503.

Ebolaviruses cause a severe and often fatal illness with the potential for global spread. Monoclonal antibody-based treatments that have become available recently have a narrow therapeutic spectrum and are ineffective against ebolaviruses other than Ebola virus (EBOV), including medically important Bundibugyo (BDBV) and Sudan (SUDV) viruses. Here, we report the development of a therapeutic cocktail comprising two broadly neutralizing human antibodies, rEBOV-515 and rEBOV-442, that recognize non-overlapping sites on the ebolavirus glycoprotein (GP). Antibodies in the cocktail exhibited synergistic neutralizing activity, resisted viral escape, and possessed differing requirements for their Fc-regions for optimal in vivo activities. The cocktail protected non-human primates from ebolavirus disease caused by EBOV, BDBV, or SUDV with high therapeutic effectiveness. High-resolution structures of the cocktail antibodies in complex with GP revealed the molecular determinants for neutralization breadth and potency. This study provides advanced preclinical data to support clinical development of this cocktail for pan-ebolavirus therapy.

Endogenous cytoplasmic DNA (cytoDNA) species are emerging as key mediators of inflammation in diverse physiological and pathological contexts. Although the role of endogenous cytoDNA in innate immune activation is well established, the cytoDNA species themselves are often poorly characterized and difficult to distinguish, and their mechanisms of formation, scope of function and contribution to disease are incompletely understood. Here, we summarize current knowledge in this rapidly progressing field with emphases on similarities and differences between distinct cytoDNAs, their underlying molecular mechanisms of formation and function, interactions between cytoDNA pathways, and therapeutic opportunities in the treatment of age-associated diseases.

Comment in Cell. 2021 Oct 28;184(22):5503-5505. Nat Biotechnol. 2021 Dec;39(12):1512-1514.

Comment on Cell. 2021 Oct 28;184(22):5635-5652.e29. Cell. 2021 Oct 28;184(22):5653-5669.e25.

Comment in Cell. 2021 Oct 28;184(22):5503-5505. Nat Methods. 2021 Dec;18(12):1449. Nat Biotechnol. 2021 Dec;39(12):1512-1514. CRISPR J. 2021 Dec;4(6):773-775.

Comment in Curr Biol. 2022 Jan 10;32(1):R46-R48.

The 2021 Lasker∼Koshland Special Achievement Award will be presented to David Baltimore for an extraordinary career that has personified the combination of outstanding biomedical research and exemplary scientific statesmanship.

On the occasion of the 2021 Lasker Basic Medical Research Award to Karl Deisseroth, Peter Hegemann, and Dieter Oesterhelt (for "the discovery of light-sensitive microbial proteins that can activate or deactivate individual brain cells-leading to the development of optogenetics and revolutionizing neuroscience"), Deisseroth reflects on this international collaboration, his basic mechanistic and structural discoveries regarding microbial channels that transduce photons into ion current, the causal exploration of brain cell function, and the pressing mysteries of psychiatry.

Comment on Cell. 2021 Oct 14;184(21):5338-5356.e21.

Comment in Trends Plant Sci. 2022 Sep;27(9):834-836.

Despite remarkable clinical efficacy of immune checkpoint blockade (ICB) in cancer treatment, ICB benefits for triple-negative breast cancer (TNBC) remain limited. Through pooled in vivo CRISPR knockout (KO) screens in syngeneic TNBC mouse models, we found that deletion of the E3 ubiquitin ligase Cop1 in cancer cells decreases secretion of macrophage-associated chemokines, reduces tumor macrophage infiltration, enhances anti-tumor immunity, and strengthens ICB response. Transcriptomics, epigenomics, and proteomics analyses revealed that Cop1 functions through proteasomal degradation of the C/ebpδ protein. The Cop1 substrate Trib2 functions as a scaffold linking Cop1 and C/ebpδ, which leads to polyubiquitination of C/ebpδ. In addition, deletion of the E3 ubiquitin ligase Cop1 in cancer cells stabilizes C/ebpδ to suppress expression of macrophage chemoattractant genes. Our integrated approach implicates Cop1 as a target for improving cancer immunotherapy efficacy in TNBC by regulating chemokine secretion and macrophage infiltration in the tumor microenvironment.

Truly creative works of science and art produce unexpected and surprising results-just like the punch line of a good joke that generates an unfamiliar twist on a familiar idea. Surprise stimulates curiosity, which triggers a search to reveal the mystery of things unknown.

Although oxidative phosphorylation is best known for producing ATP, it also yields reactive oxygen species (ROS) as invariant byproducts. Depletion of ROS below their physiological levels, a phenomenon known as reductive stress, impedes cellular signaling and has been linked to cancer, diabetes, and cardiomyopathy. Cells alleviate reductive stress by ubiquitylating and degrading the mitochondrial gatekeeper FNIP1, yet it is unknown how the responsible E3 ligase CUL2FEM1B can bind its target based on redox state and how this is adjusted to changing cellular environments. Here, we show that CUL2FEM1B relies on zinc as a molecular glue to selectively recruit reduced FNIP1 during reductive stress. FNIP1 ubiquitylation is gated by pseudosubstrate inhibitors of the BEX family, which prevent premature FNIP1 degradation to protect cells from unwarranted ROS accumulation. FEM1B gain-of-function mutation and BEX deletion elicit similar developmental syndromes, showing that the zinc-dependent reductive stress response must be tightly regulated to maintain cellular and organismal homeostasis.

Comment in Cell. 2021 Oct 14;184(21):5301-5303.

Structural maintenance of chromosomes (SMC) complexes organize genome topology in all kingdoms of life and have been proposed to perform this function by DNA loop extrusion. How this process works is unknown. Here, we have analyzed how loop extrusion is mediated by human cohesin-NIPBL complexes, which enable chromatin folding in interphase cells. We have identified DNA binding sites and large-scale conformational changes that are required for loop extrusion and have determined how these are coordinated. Our results suggest that DNA is translocated by a spontaneous 50 nm-swing of cohesin's hinge, which hands DNA over to the ATPase head of SMC3, where upon binding of ATP, DNA is clamped by NIPBL. During this process, NIPBL "jumps ship" from the hinge toward the SMC3 head and might thereby couple the spontaneous hinge swing to ATP-dependent DNA clamping. These results reveal mechanistic principles of how cohesin-NIPBL and possibly other SMC complexes mediate loop extrusion.

Comment in Nat Rev Drug Discov. 2021 Dec;20(12):896. Cell Host Microbe. 2021 Nov 10;29(11):1599-1601.

Comment in Cancer Cell. 2021 Oct 11;39(10):1305-1307. Cell. 2021 Oct 14;184(21):5306-5308.

Comment on Cell. 2021 Oct 14;184(21):5482-5496.e28.

Comment on Cell. 2021 Oct 14;184(21):5465-5481.e16.

Erratum in Cell. 2022 Feb 3;185(3):576.

Update of bioRxiv. 2021 Mar 16;:

Many enveloped viruses require the endosomal sorting complexes required for transport (ESCRT) pathway to exit infected cells. This highly conserved pathway mediates essential cellular membrane fission events, which restricts the acquisition of adaptive mutations to counteract viral co-option. Here, we describe duplicated and truncated copies of the ESCRT-III factor CHMP3 that block ESCRT-dependent virus budding and arose independently in New World monkeys and mice. When expressed in human cells, these retroCHMP3 proteins potently inhibit release of retroviruses, paramyxoviruses, and filoviruses. Remarkably, retroCHMP3 proteins have evolved to reduce interactions with other ESCRT-III factors and have little effect on cellular ESCRT processes, revealing routes for decoupling cellular ESCRT functions from viral exploitation. The repurposing of duplicated ESCRT-III proteins thus provides a mechanism to generate broad-spectrum viral budding inhibitors without blocking highly conserved essential cellular ESCRT functions.

Comment in Cell. 2021 Oct 14;184(21):5303-5305. Mol Ther. 2021 Nov 3;29(11):3097-3098. Mol Ther. 2022 Mar 2;30(3):986-987. Mol Ther. 2022 Mar 2;30(3):982-986.

This year's Lasker∼Debakey Clinical Research Award honors Katalin Karikó and Drew Weissman for the development of a therapeutic technology based on nucleoside-modification of messenger RNA, enabling the rapid development of the highly effective COVID-19 vaccines.

Erratum in Cell. 2021 Oct 28;184(22):5687-5689.