Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, which can be applied to whole-genome sequencing data from ...one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations. We introduce a principled phylogenic correction for VAFs in loci affected by copy number alterations and we show that this correction greatly improves subclonal reconstruction compared to existing methods. PhyloWGS is free, open-source software, available at https://github.com/morrislab/phylowgs.
Combination chemotherapy, either modified FOLFIRINOX (mFFX) or gemcitabine-nabpaclitaxel, are used in the treatment of most patients with advanced pancreatic ductal adenocarcinoma (PDAC), yet robust ...biomarkers of outcome are currently lacking to guide regimen selection. Here, we tested GATA6 immunohistochemistry (IHC) as a putative biomarker in advanced PDAC. GATA6 is a transcription factor in normal pancreas development. Two pathologists, blinded to clinical and molecular data, independently assessed GATA6 IHC in biopsy specimens of 130 patients with advanced PDAC, in 2 distinct phases (without and with computer assistance using the open source software QuPath). Low GATA6 IHC expression was associated with shorter overall survival median OS 6.2 months for patients with GATA6 low tumors vs. 11.5 months for patients with GATA6 high tumors, HR 1.66 (95% CI 1.15-2.40), P = 0.007. Progression appears to be higher in GATA6-low tumors compared to GATA6-high tumors in patients treated with mFFX (P = 0.024) but not in patients treated with gemcitabine regimens. GATA6 IHC expression was significantly associated with molecular subtypes (P = 0.0003). Digital assistance markedly improved interrater concordance (Cohen's kappa scores of 0.32 vs. 0.95). Our results provide strong evidence that GATA6 IHC can be used as a single biomarker in the clinic to predict clinical outcome in advanced PDAC, warranting further investigation in prospective clinical trials. These results provide the basis for an improved classification of PDAC and future biomarker design using digital pathology workflow.
Minimizing the thermal contact resistance (TCR) at the boundary between two bodies in contact is critical in diverse thermal transport devices. Conventional thermal contact methods have several ...limitations, such as high TCR, low interfacial adhesion, a requirement for high external pressure, and low optical transparency. Here, a self‐interfacing flexible thermal device (STD) that can form robust van der Waals mechanical contact and low‐resistant thermal contact to planar and non‐planar substrates without the need for external pressure or surface modification is presented. The device is based on a distinctive integration of a bioinspired adhesive architecture and a thermal transport layer formed from percolating silver nanowire (AgNW) networks. The proposed device exhibits a strong attachment (maximum 538.9 kPa) to target substrates while facilitating thermal transport across the contact interface with low TCR (0.012 m2 K kW−1) without the use of external pressure, thermal interfacial materials, or surface chemistries.
A self‐interfacing flexible thermal device that can form robust mechanical and low‐resistant thermal contact with planar and non‐planar substrates without the need for external pressure or surface modification is presented. Based on a distinctive integration of a bioinspired adhesive architecture and percolating silver nanowire networks, the proposed device exhibits a strong attachment to target substrates while facilitating efficient thermal transport.
Mitochondrial fitness and cancer risk Kossenkov, Andrew V; Milcarek, Andrew; Notta, Faiyaz ...
PloS one,
10/2022, Letnik:
17, Številka:
10
Journal Article
Recenzirano
Odprti dostop
Changes in metabolism are a hallmark of cancer, but molecular signatures of altered bioenergetics to aid in clinical decision-making do not currently exist. We recently identified a group of human ...tumors with constitutively reduced expression of the mitochondrial structural protein, Mic60, also called mitofilin or inner membrane mitochondrial protein (IMMT). These Mic60-low tumors exhibit severe loss of mitochondrial fitness, paradoxically accompanied by increased metastatic propensity and upregulation of a unique transcriptome of Interferon (IFN) signaling and Senescence-Associated Secretory Phenotype (SASP). Here, we show that an optimized, 11-gene signature of Mic60-low tumors is differentially expressed in multiple malignancies, compared to normal tissues, and correlates with poor patient outcome. When analyzed in three independent patient cohorts of pancreatic ductal adenocarcinoma (PDAC), the Mic60-low gene signature was associated with aggressive disease variants, local inflammation, FOLFIRINOX failure and shortened survival, independently of age, gender, or stage. Therefore, the 11-gene Mic60-low signature may provide an easily accessible molecular tool to stratify patient risk in PDAC and potentially other malignancies.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A macroscopic film (2.5 cm × 2.5 cm) made by layer‐by‐layer assembly of 100 single‐layer polycrystalline graphene films is reported. The graphene layers are transferred and stacked one by one using a ...wet process that leads to layer defects and interstitial contamination. Heat‐treatment of the sample up to 2800 °C results in the removal of interstitial contaminants and the healing of graphene layer defects. The resulting stacked graphene sample is a freestanding film with near‐perfect in‐plane crystallinity but a mixed stacking order through the thickness, which separates it from all existing carbon materials. Macroscale tensile tests yields maximum values of 62 GPa for the Young's modulus and 0.70 GPa for the fracture strength, significantly higher than has been reported for any other macroscale carbon films; microscale tensile tests yield maximum values of 290 GPa for the Young's modulus and 5.8 GPa for the fracture strength. The measured in‐plane thermal conductivity is exceptionally high, 2292 ± 159 W m−1 K−1 while in‐plane electrical conductivity is 2.2 × 105 S m−1. The high performance of these films is attributed to the combination of the high in‐plane crystalline order and unique stacking configuration through the thickness.
Stacked chemical vapor deposition (CVD) graphene when heat‐treated results in a macroscale graphitic film with mixed AB/incommensurate stacking through each layer but near‐perfect in‐plane order. This graphitic film has mechanical performance greatly exceeding all macroscale layered graphitic films, and an exceptionally high in‐plane thermal conductivity.
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.
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•PDAC regional heterogeneity stems from sub-tumor microenvironments (subTMEs)•SubTMEs exhibit distinct immune phenotypes and CAF differentiation states•SubTMEs execute distinct tumor-promoting and chemoprotective functions•Intratumoral subTME co-occurrence links stromal heterogeneity to patient outcome
Intratumoral heterogeneity in the human pancreatic tumor microenvironment is not random but originates in well-definable regional tissue states. The underlying sub-tumor microenvironments shape regional epithelial and immune phenotypes and influence key clinical metrics of disease progression.
To determine the impact of basal-like and classical subtypes in advanced pancreatic ductal adenocarcinoma (PDAC) and to explore GATA6 expression as a surrogate biomarker.
Within the COMPASS trial, ...patients proceeding to chemotherapy for advanced PDAC undergo tumor biopsy for RNA-sequencing (RNA-seq). Overall response rate (ORR) and overall survival (OS) were stratified by subtypes and according to chemotherapy received. Correlation of
with the subtypes using gene expression profiling,
hybridization (ISH) was explored.
Between December 2015 and May 2019, 195 patients (95%) had enough tissue for RNA-seq; 39 (20%) were classified as basal-like and 156 (80%) as classical. RECIST response data were available for 157 patients; 29 basal-like and 128 classical where the ORR was 10% versus 33%, respectively (
= 0.02). In patients with basal-like tumors treated with modified FOLFIRINOX (
= 22), the progression rate was 60% compared with 15% in classical PDAC (
= 0.0002). Median OS in the intention-to-treat population (
= 195) was 9.3 months for classical versus 5.9 months for basal-like PDAC (HR, 0.47; 95% confidence interval, 0.32-0.69;
= 0.0001).
expression by RNA-seq highly correlated with the classifier (
< 0.001) and ISH predicted the subtypes with sensitivity of 89% and specificity of 83%. In a multivariate analysis, GATA6 expression was prognostic (
= 0.02). In exploratory analyses, basal-like tumors, could be identified by keratin 5, were more hypoxic and enriched for a T-cell-inflamed gene expression signature.
The basal-like subtype is chemoresistant and can be distinguished from classical PDAC by GATA6 expression.
.
To describe the clinical, pathological and genomic characteristics of pancreatic cancer with DNA mismatch repair deficiency (MMRD) and proficiency (MMRP).
We identified patients with MMRD and MMRP ...pancreatic cancer in a clinical cohort (N=1213, 519 with genetic testing, 53 with immunohistochemistry (IHC)) and a genomic cohort (N=288 with whole-genome sequencing (WGS)).
12 out of 1213 (1.0%) in the clinical cohort were MMRD by IHC or WGS. Of the 14 patients with Lynch syndrome, 3 (21.4%) had an MMRP pancreatic cancer by IHC, and 4 (28.6%) were excluded because tissue was unavailable for testing. MMRD cancers had longer overall survival after surgery (weighted HR after coarsened exact matching 0.11, 95% CI 0.02 to 0.78, p=0.001). One patient with an unresectable MMRD cancer has an ongoing partial response 3 years after starting treatment with PD-L1/CTLA-4 inhibition. This tumour showed none of the classical histopathological features of MMRD. 9 out of 288 (3.1%) tumours with WGS were MMRD. Despite markedly higher tumour mutational burden and neoantigen loads, MMRD cancers were significantly less likely to have mutations in usual pancreatic cancer driver genes like
and
, but more likely to have mutations in genes that drive cancers with microsatellite instability like
and
. MMRD tumours were significantly more likely to have a basal-like transcriptional programme and elevated transcriptional markers of immunogenicity.
MMRD pancreatic cancers have distinct clinical, pathological and genomic profiles. Patients with MMRD pancreatic cancer should be considered for basket trials targeting enhanced immunogenicity or the unique genomic drivers in these malignancies.
To perform real-time whole genome sequencing (WGS) and RNA sequencing (RNASeq) of advanced pancreatic ductal adenocarcinoma (PDAC) to identify predictive mutational and transcriptional features for ...better treatment selection.
Patients with advanced PDAC were prospectively recruited prior to first-line combination chemotherapy. Fresh tumor tissue was acquired by image-guided percutaneous core biopsy for WGS and RNASeq. Laser capture microdissection was performed for all cases. Primary endpoint was feasibility to report WGS results prior to first disease assessment CT scan at 8 weeks. The main secondary endpoint was discovery of patient subsets with predictive mutational and transcriptional signatures.
Sixty-three patients underwent a tumor biopsy between December 2015 and June 2017. WGS and RNASeq were successful in 62 (98%) and 60 (95%), respectively. Genomic results were reported at a median of 35 days (range, 19-52 days) from biopsy, meeting the primary feasibility endpoint. Objective responses to first-line chemotherapy were significantly better in patients with the classical PDAC RNA subtype compared with those with the basal-like subtype (
= 0.004). The best progression-free survival was observed in those with classical subtype treated with m-FOLFIRINOX.
expression in tumor measured by RNA
hybridization was found to be a robust surrogate biomarker for differentiating classical and basal-like PDAC subtypes. Potentially actionable genetic alterations were found in 30% of patients.
Prospective genomic profiling of advanced PDAC is feasible, and our early data indicate that chemotherapy response differs among patients with different genomic/transcriptomic subtypes.
.
The molecular drivers of antitumor immunity in pancreatic ductal adenocarcinoma (PDAC) are poorly understood, posing a major obstacle for the identification of patients potentially amenable for ...immune-checkpoint blockade or other novel strategies. Here, we explore the association of chemokine expression with effector T-cell infiltration in PDAC.
Discovery cohorts comprised 113 primary resected PDAC and 107 PDAC liver metastases. Validation cohorts comprised 182 PDAC from The Cancer Genome Atlas and 92 PDACs from the Australian International Cancer Genome Consortium. We explored associations between immune cell counts by immunohistochemistry, chemokine expression, and transcriptional hallmarks of antitumor immunity by RNA sequencing (RNA-seq), and mutational burden by whole-genome sequencing.
Among all known human chemokines, a coregulated set of four (
, and
) was strongly associated with CD8
T-cell infiltration (
< 0.001). Expression of this "4-chemokine signature" positively correlated with transcriptional metrics of T-cell activation (
, and
), cytolytic activity (
and
), and immunosuppression (
, and
). Furthermore, the 4-chemokine signature marked tumors with increased T-cell activation scores (MHC I presentation, T-cell/APC costimulation) and elevated expression of innate immune sensing pathways involved in T-cell priming (STING and NLRP3 inflammasome pathways, BATF3-driven dendritic cells). Importantly, expression of this 4-chemokine signature was consistently indicative of a T-cell-inflamed phenotype across primary PDAC and PDAC liver metastases.
A conserved 4-chemokine signature marks resectable and metastatic PDAC tumors with an active antitumor phenotype. This could have implications for the appropriate selection of PDAC patients in immunotherapy trials.
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