Molecular Mechanisms of Intratumoral Nerve Recruitment and Perineural Invasion Elucidated with Spatial Transcriptomics and CRISPR Activation

PURPOSE/OBJECTIVE(S)

Perineural invasion (PNI) is an aggressive manifestation of tumor-nerve interactions associated with postoperative recurrence, metastasis, pain, and decreased survival. Hence, PNI is included in the staging criteria of several malignancies and often an indication for treatment intensification using adjuvant radiotherapy. However, the diverse molecular mechanisms underlying tumor-nerve crosstalk remain largely unknown-hindering the development of new therapies targeting this key pathological process. Moreover, prior studies were limited by a lack of cell-type information, spatial context, and/or a fragmented focus on a small number of pathways.

MATERIALS/METHODS

Using pancreatic ductal adenocarcinoma (PDAC) as an exemplar given the exceptionally high frequency of PNI in this malignancy, we performed the first comprehensive, cell-type specific, and spatially resolved whole-transcriptome analysis of human PDAC to identify molecular mediators of tumor-nerve crosstalk and PNI. We constructed 12 custom tissue microarrays (TMAs) derived from matched malignant regions with and without tumor-nerve proximity (n = 288 cores). We performed whole-transcriptome digital spatial profiling (DSP) to independently determine mRNA abundance from the malignant, fibroblast, and nerve compartments through optical sectioning.

RESULTS

We mapped malignant subtypes we previously identified onto the spatial data and found strong (p<0.0001) positive nerve associations with the mesenchymal, basaloid, and neural-like progenitor subtypes and a negative nerve association with the classical subtype. Numerous genes expressed by malignant cells were enriched (e.g., MMP2, PLXND1, NRP1) or depleted (e.g., SEMA3B) in association with radial distance from nerves, including recapitulation of prior literature. To functionally explore these candidate mediators of tumor-nerve crosstalk, we derived genetically-engineered murine organoids (KrasLSL-G12D/+; Trp53FL/FL; Rosa26-dCas9-VPR) and transduced them with guide RNAs to overexpress subtype-specific transcription factors or candidate genes from the spatial analysis. We quantified (1) cancer cell invasion through extracellular matrix using cultured dorsal root ganglia (DRG) sensory neurons as the chemoattractant, and (2) the role of cancer-intrinsic signaling on nerve recruitment/outgrowth by applying conditioned media or exogenous proteins to cultured DRG sensory neurons and tracking their growth with live imaging.

CONCLUSION

Our results suggest that the mechanisms enabling cancer cells to recruit nerves into the tumor microenvironment are distinct from those facilitating perineural invasion. This study has transformed our understanding of how cancer cells and the peripheral nervous system collaborate to promote tumor growth, survival, and dissemination, and is now guiding prioritization of therapeutic strategies that synergize with adjuvant radiotherapy in the burgeoning field of cancer neuroscience.

Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis

In combination with cell intrinsic properties, interactions in the tumor microenvironment modulate therapeutic response. We leveraged high-plex single-cell spatial transcriptomics to dissect the remodeling of multicellular neighborhoods and cell-cell interactions in human pancreatic cancer associated with specific malignant subtypes and neoadjuvant chemotherapy/radiotherapy. We developed Spatially Constrained Optimal Transport Interaction Analysis (SCOTIA), an optimal transport model with a cost function that includes both spatial distance and ligand-receptor gene expression. Our results uncovered a marked change in ligand-receptor interactions between cancer-associated fibroblasts and malignant cells in response to treatment, which was supported by orthogonal datasets, including an ex vivo tumoroid co-culture system. Overall, this study demonstrates that characterization of the tumor microenvironment using high-plex single-cell spatial transcriptomics allows for identification of molecular interactions that may play a role in the emergence of chemoresistance and establishes a translational spatial biology paradigm that can be broadly applied to other malignancies, diseases, and treatments.

Measurement of Cosmic Ray and Trapped Proton LET Spectra on the STS-95 HOST Mission

This paper reports on in situ measurements of the Linear-Energy-Transfer (LET) spectra of galactic cosmic rays and their progeny and of trapped Van Allen belt protons as recorded by a Pulse Height Analyzer (PHA) radiation spectrometer which flew on the STS-95 DISCOVERY mission on the Hubble Orbital Systems Test (HOST) cradle. The Shuttle was launched on 29 October 1998 and had a mission duration of 8.5 days during the minimum phase of the solar activity cycle. The orbit of the STS-95 was about 550 km altitude and 28.5° inclination. Close agreement was seen between radiation environment model predictions and the measurements of the PHA. Agreement is obtained by considering the directionality of the radiation interacting with the Shuttle structure.

Unrecognized Benign Paroxysmal Positional Vertigo in Elderly Patients

Balance disorders in elderly patients are associated with an increased risk of falls but are often difficult to diagnose because of comorbid chronic medical problems. We performed a cross-sectional study to determine the prevalence of unrecognized benign paroxysmal positional vertigo (BPPV) and associated lifestyle sequelae in a public, inner-city geriatric population. Dizziness was found in 61% of patients, whereas balance disorders were found in 77% of patients. Nine percent were found to have unrecognized BPPV. Multivariate analysis demonstrated that the presence of a spinning sensation and the absence of a lightheadedness sensation predicted the presence of unrecognized BPPV. Patients with unrecognized BPPV were more likely to have reduced activities of daily living scores, to have sustained a fall in the previous 3 months, and to have depression. These data indicate that unrecognized BPPV is common within the elderly population and has associated morbidity. Further prospective studies are warranted.

Role of subchondral bone during early-stage experimental TMJ osteoarthritis

Temporomandibular joint osteoarthritis (TMJ OA) is a degenerative disease that affects both cartilage and subchondral bone. We used microarray to identify changes in gene expression levels in the TMJ during early stages of the disease, using an established TMJ OA genetic mouse model deficient in 2 extracellular matrix proteins, biglycan and fibromodulin (bgn(-/0)fmod(-/-)). Differential gene expression analysis was performed with RNA extracted from 3-week-old WT and bgn(-/0)fmod(-/-) TMJs with an intact cartilage/subchondral bone interface. In total, 22 genes were differentially expressed in bgn(-/0)fmod(-/-) TMJs, including 5 genes involved in osteoclast activity/differentiation. The number of TRAP-positive cells were three-fold higher in bgn(-/0)fmod(-/-) TMJs than in WT. Quantitative RT-PCR showed up-regulation of RANKL and OPG, with a 128% increase in RANKL/OPG ratio in bgn(-/0)fmod(-/-) TMJs. Histology and immunohistochemistry revealed tissue disorganization and reduced type I collagen in bgn(-/0)fmod(-/-) TMJ subchondral bone. Early changes in gene expression and tissue defects in young bgn(-/0)fmod(-/-) TMJ subchondral bone are likely attributed to increased osteoclast activity. Analysis of these data shows that biglycan and fibromodulin are critical for TMJ subchondral bone integrity and reveal a potential role for TMJ subchondral bone turnover during the initial early stages of TMJ OA disease in this model.

Oxidised, glycated LDL selectively influences tissue inhibitor of metalloproteinase-3 gene expression and protein production in human retinal capillary pericytes

AIMS/HYPOTHESIS

Matrix metalloproteinases (MMPs) and their natural inhibitors, tissue inhibitor of metalloproteinases (TIMPs), regulate important biological processes including the homeostasis of the extracellular matrix, proteolysis of cell surface proteins, proteinase zymogen activation, angiogenesis and inflammation. Studies have shown that their balance is altered in retinal microvascular tissues in diabetes. Since LDLs modified by oxidation/glycation are implicated in the pathogenesis of diabetic vascular complications, we examined the effects of modified LDL on the gene expression and protein production of MMPs and TIMPs in retinal pericytes.

METHODS

Quiescent human retinal pericytes were exposed to native LDL (N-LDL), glycated LDL (G-LDL) and heavily oxidised and glycated LDL (HOG-LDL) for 24 h. We studied the expression of the genes encoding MMPs and TIMPs mRNAs by analysis of microarray data and quantitative PCR, and protein levels by immunoblotting and ELISA.

RESULTS

Microarray analysis showed that MMP1, MMP2, MMP11, MMP14 and MMP25 and TIMP1, TIMP2, TIMP3 and TIMP4 were expressed in pericytes. Of these, only TIMP3 mRNA showed altered regulation, being expressed at significantly lower levels in response to HOG- vs N-LDL. Quantitative PCR and immunoblotting of cell/matrix proteins confirmed the reduction in TIMP3 mRNA and protein in response to HOG-LDL. In contrast to cellular TIMP3 protein, analysis of secreted TIMP1, TIMP2, MMP1 and collagenase activity indicated no changes in their production in response to modified LDL. Combined treatment with N- and HOG-LDL restored TIMP3 mRNA expression to a level comparable with that after N-LDL alone.

CONCLUSIONS/INTERPRETATION

Among the genes encoding for MMPs and TIMPs expressed in retinal pericytes, TIMP3 is uniquely regulated by HOG-LDL. Reduced TIMP3 expression might contribute to microvascular abnormalities in diabetic retinopathy.

Cubilin and megalin: partners in lipoprotein and vitamin metabolism

Members of the low-density lipoprotein receptor (LDLR) family are unrivalled for their ability to endocytose and target ligands to lysosomes for degradation. Their endocytic and catabolic functions make them essential to homeostatic regulation of the level and activity of their ligands in biological fluids and interstitial spaces. Over the last few years it has become evident that the endocytic function of members of the LDLR family is employed by other kinds of cell surface receptors. Recently, the low-density lipoprotein receptor related protein-2 (megalin) was shown to act in concert with cubilin, a receptor for high-density lipoproteins (HDL)/apolipoprotein A-I (apoA-I), intrinsic factor-vitamin B12 and albumin to mediate ligand endocytosis. In this article, we review the state of knowledge pertaining to cubilin and megalin, emphasizing their joint roles in both lipoprotein and vitamin metabolism.

Unrecognized benign paroxysmal positional vertigo in elderly patients

Balance disorders in elderly patients are associated with an increased risk of falls but are often difficult to diagnose because of comorbid chronic medical problems. We performed a cross-sectional study to determine the prevalence of unrecognized benign paroxysmal positional vertigo (BPPV) and associated lifestyle sequelae in a public, inner-city geriatric population. Dizziness was found in 61% of patients, whereas balance disorders were found in 77% of patients. Nine percent were found to have unrecognized BPPV. Multivariate analysis demonstrated that the presence of a spinning sensation and the absence of a lightheadedness sensation predicted the presence of unrecognized BPPV. Patients with unrecognized BPPV were more likely to have reduced activities of daily living scores, to have sustained a fall in the previous 3 months, and to have depression. These data indicate that unrecognized BPPV is common within the elderly population and has associated morbidity. Further prospective studies are warranted.

Megalin acts in concert with cubilin to mediate endocytosis of high density lipoproteins

Cubilin has recently been shown to function as an endocytic receptor for high density lipoproteins (HDL). The lack of apparent transmembrane and cytoplasmic domains in cubilin raises questions as to the means by which it can mediate endocytosis. Since cubilin has been reported to bind the endocytic receptor megalin, we explored the possibility that megalin acts in conjunction with cubilin to mediate HDL endocytosis. While megalin did not bind to HDL, delipidated HDL, or apoA-I, it was found to copurify with cubilin isolated by HDL-Sepharose affinity chromatography. Cubilin and megalin exhibited coincident patterns of mRNA expression in mouse tissues including the kidney, ileum, thymus, placenta, and yolk sac endoderm. The expression of both receptors in yolk sac endoderm-like cells was inducible by retinoic acid treatment but not by conditions of sterol depletion. Suppression of megalin activity or expression by treatment with either megalin antibodies or megalin antisense oligodeoxynucleotides resulted in inhibition of cubilin-mediated endocytosis of HDL. Furthermore, megalin antisense oligodeoxynucleotide treatment resulted in reduced cell surface expression of cubilin. These data demonstrate that megalin acts together with cubilin to mediate HDL endocytosis and further suggest that megalin may play a role in the intracellular trafficking of cubilin.

Identification of chicken and C. elegans fibulin-1 homologs and characterization of the C. elegans fibulin-1 gene

Fibulin-1, a member of the emerging family of fibulin proteins, is a component of elastic extracellular matrix fibers, basement membranes and blood. Homologs of fibulin-1 have been described in man, mouse and zebrafish. In this study, we describe the isolation and sequencing of chicken fibulin-1C and D cDNA variants. We also describe identification of a C. elegans cDNA encoding fibulin-1D and cosmids containing the C. elegans fibulin-1 gene. Using the cDNA, RT-PCR and computer-based analysis of genomic sequences, the exon/intron organization of the C. elegans fibulin-1 gene was determined. The C. elegans fibulin-1 gene is located on chromosome IV, is approximately 6 kb in length, contains 16 exons and encodes fibulin-1C and D variants. Comparative analysis of the deduced amino acid sequences of nematode and chicken fibulin-1 variants with other known vertebrate fibulin-1 polypeptides showed that the number and organization of structural modules are identical. The results of this study indicate that the structure of the fibulin-1 protein has remained highly conserved over a large period of evolution, suggestive of functional conservation.

An Oct-like binding factor regulates Myf-5 expression in primary avian cells

Myogenic regulatory factors (MRFs) are hierarchical regulators of skeletal myogenesis. Many MRF promoters have been well characterized with respect to flanking sequences that control their expression. Yet the promoter elements that regulate Myf-5, the first MRF expressed during mammalian embryogenesis, are still largely unknown. Comparison of Myf-5 5' flanking regions from bovine, mouse, and chicken genes revealed three evolutionarily conserved elements proximal to the transcription start site: the TATA box, an octamer motif, termed OLS, and a 6-bp C-rich element. Mobility shift assays and DNase I footprinting analysis demonstrated that a nuclear factor(s) present in both bovine and avian muscle and nonmuscle tissues specifically recognized OLS. Furthermore, this binding activity reacted with a polyclonal Oct-1 antibody. In avian primary myoblast and fibroblast cultures, CAT reporter constructs under regulation of the proximal Myf-5 5' flanking sequence were expressed preferentially in myoblasts with CAT levels approximately 12-fold higher than in fibroblasts. The TATA box and octamer motif were important for expression in both myoblasts and fibroblasts: loss of the TATA box abolished activity, and disruption of the OLS resulted in 50-75% loss of promoter activity.

The low earth orbit environment observed using CREAM and CREDO

The Cosmic Radiation Environment and Dosimetry experiment (CREDO) has been operational on board the Advanced Photovoltaics & Electronics Experiment Spacecraft since August 1994. Extensive measurements of cosmic ray linear energy transfer spectra (using data to January 1996) and total dose (using data to November 1994) have been made, and compared with predictions of standard models. Detailed consideration of spacecraft shielding effects have been made. Predictions are shown to overestimate the measured linear energy transfer spectra. The CREAM experiment was flown on STS-63 in the SpaceHab module. Results show penetration of high energy electrons into the SpaceHab module.

Dexamethasone-mediated induction of MMTV-myf5 in DD3 myoblasts increases endogenous myogenin expression but does not transactivate myf5

DD3 cells are a myoblast line generated by stable transfection of C3H10T1/2 fibroblasts with the bovine myf5 cDNA (bmyf) fused to the dexamethasone-inducible MMTV promoter. After treating proliferating cells with dexamethasone, bmyf transcripts were induced approximately fivefold within 1.5-2.5 h. Induction of bmyf was followed 4 h later by a similar increase in myogenin transcripts which was dependent on protein synthesis. The elevated level of myogenin transcripts in dividing cells was comparable to that observed in DD3 myoblasts after differentiation. The 4-h lag before the myogenin response suggested involvement of an intermediate factor. However, one possible factor, myocyte-specific enhancer binding factor (MEF-2) (a known enhancer of myogenin promoter activity) was neither detectable nor inducible by dexamethasone in proliferating cells. myoD transcripts were barely detectable and uninducible in proliferating cells but strongly upregulated during differentiation. There was also a transient twofold increase in mrf4 transcripts by dexamethasone treatment in dividing cells, while no changes were detected in the levels of Id, E12, or TnC messages. The mouse myf5 gene was silent and uninducible in DD3 cells under proliferating and differentiating conditions. We conclude that ectopic expression of MMTV-bmyf led to activation of three of the endogenous myogenic factor genes of which only myogenin showed a rapid and sustained response to dexamethasone-mediated induction of bmyf in dividing cells.

Isolation, sequence, and characterization of the bovine myogenic factor-encoding gene myf-5

We report here the isolation, sequencing, and characterization of the bovine homologue of the myogenic factor-encoding gene myf-5 (termed bmyf). The transcription unit of the gene is 4.2 kb in length and contains two introns. Primer extension experiments mapped the transcription start point at 158 bp upstream from the predicted start codon and 29 bp downstream from a canonical TATA box. The 3' untranslated region contains four AATAAA sites, three of which are used to produce transcripts of 1.5, 2, and 3 kb in bovine fetal muscle RNA.

Incised grids: enhancing the readability of tangible graphs for the blind

The transformation of a graphic display into tangible form for blind persons is usually achieved by raising the entire image above the surface. In the case of tangible line graphs, this format causes readability problems by degrading figure-ground (data-curve/grid) differentiation. This study assessed the feasibility of a new design format involving both raised and incised elements in the same display. The results from 24 blind students in grades 4 through 7 indicated that an incised-grid/raised-data-curve format significantly improves graph-reading performance relative to a raised-grid/raised-data-curve format. The importance of designing displays in ways that are compatible with the perceptual-motor capabilities of blind persons is discussed.