Multifunctional Optical Tomography System With High-Fidelity Surface Extraction Based on a Single Programmable Scanner and Unified Pinhole Modeling.

OBJECTIVE: Macroscopic optical tomography is a non-invasive method that can visualize the 3D distribution of intrinsic optical properties or exogenous fluorophores, making it highly attractive for small animal imaging. However, reconstructing the images requires prior knowledge of surface information. To address this, existing systems often use additional hardware components or integrate multimodal information, which is expensive and introduces new issues such as image registration. Our goal is to develop a multifunctional optical tomography system that can extract surface information using a concise hardware design. METHODS: Our proposed system uses a single programmable scanner to implement both surface extraction and optical tomography functions. A unified pinhole model is used to describe both the illumination and detection procedures for capturing 3D point cloud. Line-shaped scanning is adopted to improve both spatial resolution and speed of surface extraction. Finally, we integrate the extracted surface information into the optical tomographic reconstruction to more accurately map the fluorescence distribution. RESULT: Comprehensive phantom experiments with different levels of complexity were designed to evaluate the performance of surface extraction and fluorescence tomography. We also imaged the axillary lymph nodes in living mice after injection of fluorophore, demonstrating the proposed system facilitates more reliable fluorescence tomography. CONCLUSION: We have successfully developed a versatile optical tomography system by leveraging concise hardware design and unified pinhole modeling. Phantom validation demonstrates that our system provides high-precision surface information with a maximum error of 0.1 mm, while the surface-guided FMT reconstruction is more reliable than the blind reconstruction using simplified surface geometry, elevating several quantitative metrics including RMSE, CNR, and Dice. SIGNIFICANCE: Our work explores the feasibility of obtaining additional surface information using existing components of standalone optical tomography. This makes the optical tomographic technique more accurate and more accessible to biomedical researchers.

Identification of m6A-related lncRNAs for thyroid cancer recurrence.

Background: Although the prognosis of thyroid cancer (THCA) is generally good, many patients have a high risk of recurrence after treatment. N6-methyladenosine (m6A)-related long noncoding RNAs (lncRNAs) have been extensively studied in recent years. However, the potential of m6A-related lncRNAs to predict recurrence in THCA is unknown. Methods: RNA sequencing (RNA-seq) data and clinical information for THCA were downloaded from The Cancer Genome Atlas (TCGA). Differentially expressed lncRNAs (DELs) were identified using the R package DESeq2. A coexpression network based on m6A-related genes and lncRNAs was constructed. The CIBERSORT algorithm and gene set enrichment analysis (GSEA) were used for immune-infiltrating cell estimation and clustering functional enrichment analysis, respectively. A Kaplan-Meier plot was used for prognostic analysis based on m6A-associated lncRNA risk patterns. The expression of lncRNAs in recurrent and nonrecurrent THCA tissues was analyzed by real-time quantitative polymerase chain reaction (RT-qPCR). Results: A network of m6A-related lncRNAs containing 8 lncRNAs was constructed with good predictive power for recurrence in THCA. A total of 3 clusters were obtained, and cluster 1 was most associated with THCA recurrence. We found significantly lower levels of CD8 T cells and follicular helper T cells, and significantly higher levels of dendritic cells (DCs), M2 macrophages, resting DCs, regulatory T cells, and mast cells in cluster 1 patients. Pathway analysis revealed significant enrichment in natural killer cell-mediated cytotoxicity, butyrate metabolism, and cell adhesion molecules in cluster 1. The m6A-related lncRNA risk model was effective in predicting progression-free survival (PFS) in patients with THCA recurrence. RT-qPCR analysis based on 40 THCA clinical samples from our center found the risk model to be a good predictor of recurrence in THCA patients. Conclusions: In summary, m6A-related lncRNAs may provide a novel predictive method for prognostic relapse in THCA patients.

Advances in targeting of miR­10­associated lncRNAs/circRNAs for the management of cancer (Review).

With advancements in sequencing technologies, an increasing number of aberrantly expressed long-non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have been identified in various types of cancer. lncRNAs and circRNAs are now well-established tumor-influencing factors in cancer, driving not only tumor proliferation and invasion, but also cancer progression, drug resistance and metastatic recurrence. The majority of lncRNAs and circRNAs influence cancer progression by targeting microRNAs (miRNAs/miRs). miR-10a and miR-10b, key members of the miR-10 family, have been shown to play important regulatory roles in cell proliferation, differentiation to cancer progression, and development. Manual evaluation and grouping according to different types of competing endogenous RNA and tumor was performed. The review outlined the current state of knowledge on the regulation of miR-10 family-related lncRNAs and circRNAs. The involvement of lncRNAs and circRNAs in the biogenesis, maturation and function of malignant tumors through the miR-10 family, and the key gene targets and signaling cascades that lncRNAs and circRNAs regulate through the miR-10 family were summarized. Based on the findings of this review, it can be hypothesized that lncRNAs and circRNAs targeting the miR-10 family may serve as diagnostic/prognostic markers and/or therapeutic targets for the management of cancer.

Ufmylation reconciles salt stress-induced unfolded protein responses via ER-phagy in Arabidopsis.

In plants, the endomembrane system is tightly regulated in response to environmental stresses for maintaining cellular homeostasis. Autophagosomes, the double membrane organelles forming upon nutrient deprivation or stress induction, degrade bulky cytosolic materials for nutrient turnover. Though abiotic stresses have been reported to induce plant autophagy, few receptors or regulators for selective autophagy have been characterized for specific stresses. Here, we have applied immunoprecipitation followed by tandem mass spectrometry using the autophagosome marker protein ATG8 as bait and have identified the E3 ligase of the ufmylation system Ufl1 as a bona fide ATG8 interactor under salt stress. Notably, core components in the ufmylation cascade, Ufl1 and Ufm1, interact with the autophagy kinase complexes proteins ATG1 and ATG6. Cellular and genetic analysis showed that Ufl1 is important for endoplasmic reticulum (ER)-phagy under persisting salt stress. Loss-of-function mutants of Ufl1 display a salt stress hypersensitive phenotype and abnormal ER morphology. Prolonged ER stress responses are detected in ufl1 mutants that phenocopy the autophagy dysfunction atg5 mutants. Consistently, expression of ufmylation cascade components is up-regulated by salt stress. Taken together, our study demonstrates the role of ufmylation in regulating ER homeostasis under salt stress through ER-phagy.

TGFß control of immune responses in cancer: a holistic immuno-oncology perspective.

The immune system responds to cancer in two main ways. First, there are prewired responses involving myeloid cells, innate lymphocytes and innate-like adaptive lymphocytes that either reside in premalignant tissues or migrate directly to tumours, and second, there are antigen priming-dependent responses, in which adaptive lymphocytes are primed in secondary lymphoid organs before homing to tumours. Transforming growth factor-ß (TGFß) - one of the most potent and pleiotropic regulatory cytokines - controls almost every stage of the tumour-elicited immune response, from leukocyte development in primary lymphoid organs to their priming in secondary lymphoid organs and their effector functions in the tumour itself. The complexity of TGFß-regulated immune cell circuitries, as well as the contextual roles of TGFß signalling in cancer cells and tumour stromal cells, necessitates the use of rigorous experimental systems that closely recapitulate human cancer, such as autochthonous tumour models, to uncover the underlying immunobiology. The diverse functions of TGFß in healthy tissues further complicate the search for effective and safe cancer therapeutics targeting the TGFß pathway. Here we discuss the contextual complexity of TGFß signalling in tumour-elicited immune responses and explain how understanding this may guide the development of mechanism-based cancer immunotherapy.

lncRNA TUG1 protects intestinal epithelial cells from damage induced by high glucose and high fat via AMPK/SIRT1.

he incidence of obesity and type 2 diabetes mellitus (T2DM) is increasing year by year and shows a trend towards younger age groups worldwide. It has become a disease that endangers the health of individuals all over the world. Among numerous weight loss surgeries, sleeve gastrectomy (SG) has become one of the most common surgical strategies for the treatment of T2DM. However, SG­mediated alterations to the molecular mechanism of metabolism require further investigation. Thus, reverse transcription­quantitative PCR was used to detect the expression levels of long non­coding (lnc)RNA taurine­upregulated gene 1 (TUG1), Sirtuin 1 (SIRT1), AMP­activated protein kinase (AMPK) and uncoupling protein 2 (UCP2) in the serum of T2DM patients, as well as in HIEC­6 and SW480 cells following treatment with high glucose and high fat (HGHF). Protein expression was detected by western blotting. Cell Counting Kit­8 assays were performed to analyze cell viability, and flow cytometry and a TUNEL assay was performed to evaluate cell apoptosis. The secretion of ILs in the culture medium was detected by conducting ELISAs. The results showed that lncRNA TUG1 and UCP2 expression was upregulated, SIRT1 and AMPK expression levels were decreased by SG. Under HGHF conditions, HIEC­6 and SW480 cell viability was inhibited, apoptosis was promoted, TUG1 expression was downregulated, and SIRT1 and AMPK expression levels were upregulated. The secretory levels of IL­1ß, IL­6 and IL­8 were increased, whereas the secretion of IL­10 was decreased under HGHF conditions. lncRNA TUG1 overexpression significantly reversed the effects of HGHF on cell viability, apoptosis and SIRT1, AMPK, UCP2 and Bcl­2 expression levels. Together, the findings of the present study demonstrated that lncRNA TUG1 alleviated the damage induced by HGHF in intestinal epithelial cells by downregulating SIRT1 and AMPK expression, and upregulating UCP2 expression. Thus, the lncRNA TUG1/AMPK/SIRT1/UCP2 axis may serve an important role in the treatment of T2DM.

Effect of GATAD1 regulating the SRRM2 gene on recurrence of thyroid tumor and its molecular mechanism.

Background: Thyroid blood vessels and nerves are rich, and their anatomical and physiological structures are complex. Surgery often fails to eradicate the tumor, which has a serious negative impact on the surgical outcomes and patient prognosis. Therefore, it is important to accurately predict the recurrence rate of thyroid cancer. Methods: Based on bioinformatics analysis, the highly expressed transcription factors and differential genes in thyroid carcinoma (THCA) were obtained. Kaplan-Meier survival analysis was used to analyze the clinical effects of GATAD1 as well as SRRM2 on the recurrence of THCA patients. The effect of GATAD1 on SRRM2 expression was explored using cell experiments. Other experiments were conducted to reveal the interaction between SRRM2 and GATAD1 and their functions in THCA progression, such as cell proliferation and cell cycle. Results: GATAD1 was overexpressed in recurrent THCA tissue compared with that in adjacent normal tissue. GATAD1 and SRRM2 were identified as the key risk factors for THCA recurrence as well as survival. Knockdown of GATAD1 and SRRM2 can inhibit THCA cell proliferation and arrest THCA cells in the G1 phase. Inhibiting GATAD1 decreased SRRM2 expression in THCA cells, whereas overexpressing GATAD1 had the opposite result. SRRM2 knockdown eliminated GATAD1-induced proliferation of THCA cells in vitro, indicating that GATAD1-induced THCA cell proliferation was dependent on increased SRRM2 expression. Conclusions: We identified GATAD1 as an underlying diagnostic biomarker in THCA recurrence patients. The GATAD1-SRRM2 axis mediates human THCA recurrence progression and is an underlying target for THCA treatment.

Immunity beyond cancer cells: perspective from tumor tissue.

Investigation of cancer as a cell-level disease has led to the development of cancer cell-directed therapies including cytotoxic T lymphocyte (CTL)-based immunotherapy; yet, many patients are refractory to these modalities of cancer treatment and acquired resistance frequently occurs. Of note, cancer environment controls the manifestation of cancerous cell phenotype. Helper T (Th) cells orchestrate immune defense responses targeting cancer cells as well as the tumor microenvironment. Recent studies have shown that in addition to interferon (IFN)-γ-producing Th1 cells, interleukin (IL)-4-producing Th2 cells function as potent anticancer effectors in part by promoting tumor stroma reconfiguration and tumor tissue repair. Such Th cell-mediated tissue-level immunity may be harnessed for novel modalities of cancer environment immunotherapy.

Gradient-Based Feature Extraction From Raw Bayer Pattern Images.

In this paper, the impact of demosaicing on gradient extraction is studied and a gradient-based feature extraction pipeline based on raw Bayer pattern images is proposed. It is shown both theoretically and experimentally that the Bayer pattern images are applicable to the central difference gradient-based feature extraction algorithms with negligible performance degradation, as long as the arrangement of color filter array (CFA) patterns matches the gradient operators. The color difference constancy assumption, which is widely used in various demosaicing algorithms, is applied in the proposed Bayer pattern image-based gradient extraction pipeline. Experimental results show that the gradients extracted from Bayer pattern images are robust enough to be used in histogram of oriented gradients (HOG)-based pedestrian detection algorithms and shift-invariant feature transform (SIFT)-based matching algorithms. By skipping most of the steps in the image signal processing (ISP) pipeline, the computational complexity and power consumption of a computer vision system can be reduced significantly.

TGF-ß suppresses type 2 immunity to cancer.

The immune system uses two distinct defence strategies against infections: microbe-directed pathogen destruction characterized by type 1 immunity1, and host-directed pathogen containment exemplified by type 2 immunity in induction of tissue repair2. Similar to infectious diseases, cancer progresses with self-propagating cancer cells inflicting host-tissue damage. The immunological mechanisms of cancer cell destruction are well defined3-5, but whether immune-mediated cancer cell containment can be induced remains poorly understood. Here we show that depletion of transforming growth factor-ß receptor 2 (TGFBR2) in CD4+ T cells, but not CD8+ T cells, halts cancer progression as a result of tissue healing and remodelling of the blood vasculature, causing cancer cell hypoxia and death in distant avascular regions. Notably, the host-directed protective response is dependent on the T helper 2 cytokine interleukin-4 (IL-4), but not the T helper 1 cytokine interferon-γ (IFN-γ). Thus, type 2 immunity can be mobilized as an effective tissue-level defence mechanism against cancer.

Cancer immunotherapy via targeted TGF-ß signalling blockade in TH cells.

Cancer arises from malignant cells that exist in dynamic multilevel interactions with the host tissue. Cancer therapies aiming to directly kill cancer cells, including oncogene-targeted therapy and immune-checkpoint therapy that revives tumour-reactive cytotoxic T lymphocytes, are effective in some patients1,2, but acquired resistance frequently develops3,4. An alternative therapeutic strategy aims to rectify the host tissue pathology, including abnormalities in the vasculature that foster cancer progression5,6; however, neutralization of proangiogenic factors such as vascular endothelial growth factor A (VEGFA) has had limited clinical benefits7,8. Here, following the finding that transforming growth factor-ß (TGF-ß) suppresses T helper 2 (TH2)-cell-mediated cancer immunity9, we show that blocking TGF-ß signalling in CD4+ T cells remodels the tumour microenvironment and restrains cancer progression. In a mouse model of breast cancer resistant to immune-checkpoint or anti-VEGF therapies10,11, inducible genetic deletion of the TGF-ß receptor II (TGFBR2) in CD4+ T cells suppressed tumour growth. For pharmacological blockade, we engineered a bispecific receptor decoy by attaching the TGF-ß-neutralizing TGFBR2 extracellular domain to ibalizumab, a non-immunosuppressive CD4 antibody12,13, and named it CD4 TGF-ß Trap (4T-Trap). Compared with a non-targeted TGF-ß-Trap, 4T-Trap selectively inhibited TH cell TGF-ß signalling in tumour-draining lymph nodes, causing reorganization of tumour vasculature and cancer cell death, a process dependent on the TH2 cytokine interleukin-4 (IL-4). Notably, the 4T-Trap-induced tumour tissue hypoxia led to increased VEGFA expression. VEGF inhibition enhanced the starvation-triggered cancer cell death and amplified the antitumour effect of 4T-Trap. Thus, targeted TGF-ß signalling blockade in helper T cells elicits an effective tissue-level cancer defence response that can provide a basis for therapies directed towards the cancer environment.