A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression.

Eukaryotic transfer RNAs can become selectively fragmented upon various stresses, generating tRNA-derived small RNA fragments. Such fragmentation has been reported to impact a small fraction of the tRNA pool and thus presumed to not directly impact translation. We report that oxidative stress can rapidly generate tyrosine-tRNAGUA fragments in human cells-causing significant depletion of the precursor tRNA. Tyrosine-tRNAGUA depletion impaired translation of growth and metabolic genes enriched in cognate tyrosine codons. Depletion of tyrosine tRNAGUA or its translationally regulated targets USP3 and SCD repressed proliferation-revealing a dedicated tRNA-regulated growth-suppressive pathway for oxidative stress response. Tyrosine fragments are generated in a DIS3L2 exoribonuclease-dependent manner and inhibit hnRNPA1-mediated transcript destabilization. Moreover, tyrosine fragmentation is conserved in C. elegans. Thus, tRNA fragmentation can coordinately generate trans-acting small RNAs and functionally deplete a tRNA. Our findings reveal the existence of an underlying adaptive codon-based regulatory response inherent to the genetic code.

Challenges and solutions to superior chimeric antigen receptor-T design and deployment for B-cell lymphomas.

Chimeric antigen receptor-T (CAR-T) therapies represent a major breakthrough in cancer medicine, given the ex vivo-based technology that harnesses the power of one's own immune system. These therapeutics have demonstrated remarkable success for relapsed/refractory B-cell lymphomas. Although more than a decade has passed since the initial introduction of CAR-T therapeutics for patients with leukaemia and lymphoma, there is still significant debate as to where CAR-T therapeutics fit into the management paradigm, as consensus guidelines are limited. Competing interventions deployed in subsequent lines of therapy for aggressive lymphoma include novel targeted agents, bispecific antibodies, and time-honoured stem cell transplant. In this focused review, we discuss the major obstacles to advancing the therapeutic reach for CAR-T products in early lines of therapy. Such barriers include antigen escape, "cold" tumour microenvironments, host inflammation and CAR-T cell exhaustion. We highlight solutions including point-of-care CAR-T manufacturing and early T lymphopheresis. We review the evidence basis for early CAR-T deployment for B-cell lymphomas in light of the recent Food and Drug Administration (FDA) approval of three first-in-class anti-CD3/CD20 bispecific antibodies-mosunetuzumab, epcoritamab and glofitamab. We propose practical recommendations for 2024.

Intra-operative tumor spillage in minimally invasive surgery for endometrial cancer and its impact on recurrence risk.

OBJECTIVE: The prognostic impact of intra-operative tumor spillage (ITS) during minimally invasive surgery (MIS) for endometrial cancer (EC) is not well studied. The objective of this study was to determine if there is an association between ITS and EC recurrence. METHODS: We performed a case-control study of patients with a laparoscopic or robot-assisted hysterectomy with EC on final pathology between 2017 and 2022 and compared those with (case) and without (control) a subsequent EC recurrence. Electronic medical records were reviewed for demographic, intra-operative and pathologic details, and recurrence status. ITS was defined as uterine perforation with a manipulator, presence of extra-uterine tumor after colpotomy or specimen delivery, exposure of uncontained specimen into peritoneum, and/or pathology/operative reports noting specimen fragmentation. Conditional logistic regression was used to determine odds ratios for the association of cancer recurrence with ITS. We adjusted for >50% myoinvasion, tumor size, and adjuvant treatment. RESULTS: 1057 patients underwent MIS for EC. Approximately 8% (n = 86) developed recurrent cancer and 172 patients were selected as controls. Twenty percent of recurrent cases (17/86) had ITS compared with 4% of nonrecurrent controls (7/172). When adjusted for tumor size, deep myoinvasion, and adjuvant treatment, patients with ITS had a 5.6 times increased odds (aOR 5.63, 95% CI 1.52-20.86) of recurrence compared to patients without ITS. CONCLUSIONS: In patients with EC, we found an association between ITS and cancer recurrence. These findings warrant further investigation to determine if adjuvant therapy or surgical technique should be altered to improve outcomes.

The shifting therapeutic paradigm for relapsed/refractory mantle cell lymphoma.

Mantle cell lymphoma (MCL) is a heterogeneous subtype of non-Hodgkin lymphoma that has been historically associated with poor 5-year overall survival rates, especially for aggressive variants. Traditional cytotoxic chemotherapy had been a mainstay of therapy for relapsed/refractory (R/R) MCL for many years until the advent of molecularly targeted therapies and cell-based approaches. However, a significant concern is the lack of definitive consensus guidelines for management of R/R MCL. The managerial conundrum partly stems from the absence of head-to-head comparisons of novel therapies, with conclusions drawn from cross-trial comparisons. In this evidence-based review, we discuss the current therapeutic options for R/R MCL, including the most recent data from the BRUIN study that led to the approval of the first-in-class non-covalent reversible Bruton's tyrosine kinase (BTK) inhibitor pirtobrutinib in 2023, as well as the recent removal of ibrutinib from the market. We discuss outlooks for targeted therapy and tolerability considerations for novel agents, including unique considerations for the elderly population. We highlight emerging data that support the curative potential of chimeric antigen receptor-T (CAR-T) therapy from ZUMA-2, relative to other promising investigational agents in the pipeline, including glofitamab, epcoritamab, and zilovertamab vedotin. We summarize management recommendations based upon the most rigorous clinical evidence to date.

Elastic fibers define embryonic tissue stiffness to enable buckling morphogenesis of the small intestine.

During embryonic development, tissues must possess precise material properties to ensure that cell-generated forces give rise to the stereotyped morphologies of developing organs. However, the question of how material properties are established and regulated during development remains understudied. Here, we aim to address these broader questions through the study of intestinal looping, a process by which the initially straight intestinal tube buckles into loops, permitting ordered packing within the body cavity. Looping results from elongation of the tube against the constraint of an attached tissue, the dorsal mesentery, which is elastically stretched by the elongating tube to nearly triple its length. This elastic energy storage allows the mesentery to provide stable compressive forces that ultimately buckle the tube into loops. Beginning with a transcriptomic analysis of the mesentery, we identified widespread upregulation of extracellular matrix related genes during looping, including genes related to elastic fiber deposition. Combining molecular and mechanical analyses, we conclude that elastin confers tensile stiffness to the mesentery, enabling its mechanical role in organizing the developing small intestine. These results shed light on the role of elastin as a driver of morphogenesis that extends beyond its more established role in resisting cyclic deformation in adult tissues.

Arginine limitation causes a directed DNA sequence evolution response in colorectal cancer cells.

Utilization of specific codons varies significantly across organisms. Cancer represents a model for understanding DNA sequence evolution and could reveal causal factors underlying codon evolution. We found that across human cancer, arginine codons are frequently mutated to other codons. Moreover, arginine restriction-a feature of tumor microenvironments-is sufficient to induce arginine codon-switching mutations in human colon cancer cells. Such DNA codon switching events encode mutant proteins with arginine residue substitutions. Mechanistically, arginine limitation caused rapid reduction of arginine transfer RNAs and the stalling of ribosomes over arginine codons. Such selective pressure against arginine codon translation induced a proteomic shift towards low arginine codon containing genes, including specific amino acid transporters, and caused mutational evolution away from arginine codons-reducing translational bottlenecks that occurred during arginine starvation. Thus, environmental availability of a specific amino acid can influence DNA sequence evolution away from its cognate codons and generate altered proteins.

Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells.

Utilization of specific codons varies between organisms. Cancer represents a model for understanding DNA sequence evolution and could reveal causal factors underlying codon evolution. We found that across human cancer, arginine codons are frequently mutated to other codons. Moreover, arginine limitation-a feature of tumor microenvironments-is sufficient to induce arginine codon-switching mutations in human colon cancer cells. Such DNA codon switching events encode mutant proteins with arginine residue substitutions. Mechanistically, arginine limitation caused rapid reduction of arginine transfer RNAs and the stalling of ribosomes over arginine codons. Such selective pressure against arginine codon translation induced an adaptive proteomic shift toward low-arginine codon-containing genes, including specific amino acid transporters, and caused mutational evolution away from arginine codons-reducing translational bottlenecks that occurred during arginine starvation. Thus, environmental availability of a specific amino acid can influence DNA sequence evolution away from its cognate codons and generate altered proteins.

De novo sphingolipid biosynthesis necessitates detoxification in cancer cells.

Sphingolipids play important signaling and structural roles in cells. Here, we find that during de novo sphingolipid biosynthesis, a toxic metabolite is formed with critical implications for cancer cell survival. The enzyme catalyzing the first step in this pathway, serine palmitoyltransferase complex (SPT), is upregulated in breast and other cancers. SPT is dispensable for cancer cell proliferation, as sphingolipids can be salvaged from the environment. However, SPT activity introduces a liability as its product, 3-ketodihydrosphingosine (3KDS), is toxic and requires clearance via the downstream enzyme 3-ketodihydrosphingosine reductase (KDSR). In cancer cells, but not normal cells, targeting KDSR induces toxic 3KDS accumulation leading to endoplasmic reticulum (ER) dysfunction and loss of proteostasis. Furthermore, the antitumor effect of KDSR disruption can be enhanced by increasing metabolic input (via high-fat diet) to allow greater 3KDS production. Thus, de novo sphingolipid biosynthesis entails a detoxification requirement in cancer cells that can be therapeutically exploited.

Visualizing microcalcifications in lumpectomy specimens: an exploration into the clinical potential of carbon nanotube-enabled stationary digital breast tomosynthesis.

PURPOSE: To assess the visibility of microcalcifications in images generated by a first-generation carbon-nanotube (CNT)-enabled stationary digital breast tomosynthesis (sDBT) device, using magnified 2D mammography and conventional, moving-source DBT as references for comparison. METHODS: Lumpectomy specimens were imaged by magnified mammography and two 3D mammography approaches, including sDBT and moving-source DBT. The planar size of individual microcalcifications was measured in the reconstructed image stacks of sDBT and moving-source DBT and compared to the magnified mammography image. An artifact spread function (ASF) was used to assess the depth dimensions of the microcalcifications displayed through the reconstructed image stacks. Breast-imaging specialists rated their preference for one imaging modality over another when interpreting microcalcifications in the magnified mammography image and synthetic slab images from sDBT and moving-source DBT. RESULTS: The planar size of individual microcalcifications was similar in images generated by sDBT and moving-source DBT when the sDBT projections were binned to match the pixel size used by the moving-source DBT system. However, the unique structure of sDBT allowed for a wider-angle span of projection views and operation of the detector in full-resolution mode without significantly compromising the scan time. In this configuration, the planar sizes of individual microcalcifications displayed by sDBT was more similar to magnified mammography than moving-source DBT, and the microcalcifications had a narrower ASF through depth. Readers preferred sDBT over moving-source DBT when assessing microcalcifications in synthetic slab images, although magnified mammography was rated highest overall. CONCLUSIONS: The sDBT system displayed microcalcifications as well as conventional, moving-source DBT when the effective pixel size of the detector was matched. However, with the detector in its full-resolution mode, sDBT displayed microcalcifications with greater clarity. Readers still preferred images generated by magnified mammography over both 3D mammography approaches. This finding is guiding continued hardware and software development to optimize the sDBT technology.