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| 2. |
- Zhang, Xueli, 1991-
(författare)
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Biomarkers for Diagnosis, Therapy and Prognosis in Colorectal Cancer : a study from databases, machine learning predictions to laboratory confirmations
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Colorectal cancer (CRC) is one of the leading causes of cancer death worldwide. Early diagnosis and better therapy response have been believed to be associated with better prognosis. CRC biomarkers are considered as precise indicators for the early diagnosis and better therapy response. It is, therefore, of importance to find out, analyze and evaluate the CRC biomarkers to further provide the more precis evidence for predicting novel potential biomarkers and eventually to improve early diagnosis, personalized therapy and prognosis for CRC.In this study, we started with creating and establishing a CRC biomarker database. (CBD: http://sysbio.suda.edu.cn/CBD/index.html) In the CBD database, there were 870 reported CRC biomarkers collected from the published articles in PubMed. In this version of the CBD, CRC biomarker data was carefully collected, sorted, displayed, and analyzed. The major applications of the CBD are to provide 1) the records of CRC biomarkers (DNA, RNA, protein and others) concerning diagnosis, treatment and prognosis; 2) the basic and clinical research information concerning the CRC biomarkers; 3) the primary results for bioinformatics and biostatics analysis of the CRC biomarkers; 4) downloading/uploading the biomedicine information for CRC biomarkers.Based on our CBD and other public databases, we further analyzed the presented CRC biomarkers (DNAs, RNAs, proteins) and predicted novel potential multiple biomarkers (the combination of single biomarkers) with biological networks and pathways analysis for diagnosis, therapy response and prognosis in CRC. We found several hub biomarkers and key pathways for the diagnosis, treatment and prognosis in CRC. Receiver operating characteristic (ROC) test and survival analysis by microarray data revealed that multiple biomarkers could be better biomarkers than the single biomarkers for the diagnosis and prognosis of CRC.There are 62 diagnosis biomarkers for colon cancer in our CBD. In the previous studies, we found these present biomarkers were not enough to improve significantly the diagnosis of colon cancer. In order to find out novel biomarkers for the colon cancer diagnosis, we have performed /machine learning (ML) techniques such as support vector machine (SVM) and regression tree to predict candidate to discover diagnostic biomarkers for colon cancer. Based on the protein-protein interaction (PPI) network topology features of the identified biomarkers, we found 12 protein biomarkers which were considered as the candidate colon cancer diagnosis biomarkers. Among these protein biomarkers Chromogranin-A (CHGA) was the most powerful biomarker, which showed good performance in bioinformatics test and Immunohistochemistry(IHC). We are now expanding this study to CRC.Expression of CHGA protein in colon cancer was further verified with a novel logistic regressionbased meta-analysis, and convinced as a valuable diagnostic biomarker as compared with the typical diagnostic biomarkers, such as TP53, KRAS and MKI67.microRNAs (miRNAs/miRs) have been considered as potential biomarkers. A novel miRNA-mRNA interaction network-based model was used to predict miRNA biomarkers for CRC and found that miRNA-186-5p, miRNA-10b-5p and miRNA-30e-5p might be the novel biomarkers for CRC diagnosis. In conclusion, we have created a useful CBD database for CRC biomarkers and provided detailed information for how to use the CBD in CRC biomarker investigations. Our studies have been focusing on the biomarkers in diagnosis, therapy and prognosis. Based on our CBD and other powerful cancer associated databases, ML has been used to analyze the characteristics of the CRC biomarkers and predict novel potential CRC biomarkers. The predicted potential biomarkers were further confirmed at biomedical laboratory.
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| 3. |
- Gnosa, Sebastian, 1984-
(författare)
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Astrocyte elevated gene-1 in relation to colorectal cancer development and radiotherapy response
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The incidence and death rate for colorectal cancer (CRC) decreased during the last decades as a result of improved diagnosis and treatment. However, CRC is still the third most common cancer in the world, and is responsible for about 700 000 deaths per year worldwide. Therefore, it is important to understand the mechanisms of the disease, and to find molecular markers in order to further improve prognosis, and to develop new treatment strategies. Astrocyte elevated gene-1 (AEG-1), encoded by the MTDH gene, is upregulated in a variety of cancers. AEG-1 is involved in cell survival, proliferation, migration, invasion, metastasis, angiogenesis, and apoptosis.The aim of this thesis was to investigate the role of AEG-1 in CRC development and the impact of AEG-1 on the response of radiation treatment. The AEG-1 expression, analysed in different CRC patient cohorts in paper I and III, was increased in the tumour tissue compared with the normal mucosa, and higher in the lymph node and liver metastases. Expression analyses in normal and cancer cell lines confirmed these results. In paper II, sequencing of the complete coding sequence of the MTDH gene in 356 patients revealed 50 single nucleotide variants of which 29 were novel. Eight exonic variants were detected, including three frameshift variants which were probably pathogenic, and two missense variants located in functional protein regions. There was no correlation of the MTDH variants or AEG-1 expression with the patient survival. In paper III, we also investigated the impact of AEG-1 on the response to radiation treatment. AEG-1 knockdown decreased the cellular survival upon radiation in several colon cancer cell lines. The AEG-1 expression was furthermore analysed in patients, which were randomised to either surgery alone or preoperative radiotherapy (RT), followed by surgery. The rectal cancer patients with high AEG-1 expression treated with RT had a significantly higher risk of developing distant recurrence and had a worse disease free survival, likely due to the metastasis promoting properties of AEG-1. In paper IV, the impact of AEG-1 knockdown and radiation on migration and invasion was analysed in colon cancer cell lines in vitro and in a novel zebrafish model in vivo. AEG-1 knockdown decreased migration and invasion, and radiation-enhanced migration and invasion in the cell lines tested.In conclusion, our data suggest that AEG-1 is involved in CRC development, while MTDH gene variants probably not have a high clinical importance in CRC. Furthermore, AEG-1 is a promising radiosensitising target and a valuable prognostic marker in CRC. We further showed that AEG-1 knockdown inhibits migration and invasion, as well as radiation-enhanced cell migration and invasion.
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| 4. |
- Fredriksson, Camilla, 1969-
(författare)
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Keratinocytes in tissue engineering of human skin: invitro and in vivo studies
- 2008
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Full thickness wounds, such as deep burns, need restoration of both the dermal and epidermal layers of the skin. In normal wound healing, re-epithelialization occurs by migration and proliferation of keratinocytes from the wound edges and by differentiation of stem cells from remaining hair follicles. Restoration of dermis occurs by influx of growth factors secreted by macrophages, platelets, and fibroblasts; by fibroblast proliferation and subsequent synthesis and remodeling of collagenous dermal matrix. In the case of full-thickness acute burn injuries and chronic wounds (e.g. pressure ulcers, venous ulcers and diabetic foot ulcers), these processes are defective. With the principles of tissue engineering in mind (to correct, improve and maintain tissues and their functions), researchers have developed promising materials and methods to make it possible to restore either the dermal (Integra® DRT, Alloderm®) or the epidermal layer (split thickness skin grafts (STSG), cultured epithelial autografts (CEA), autologous keratinocytes in single cell suspension). It is now well established that superior results are obtained if both dermal and epidermal components are combined, for example in a bilayered skin equivalent. Apligraf® is recommended for use on venous ulcers and is the only bilayered living skin equivalent currently approved by the FDA. Studies on different factors affecting the wound healing capacity as well as techniques in use provide valuable information for further development.In this licentiate thesis, we evaluated different transplantation techniques for delivering cultured human keratinocytes in single cell suspension, a measure becoming more frequently used in addition to STSG and CEA for restoring the epidermal layer of the skin. We found that the pressure device, commonly used to spray cell suspension onto the wound with pressures as high as 200 kPa, killed around 0% of the cells. In comparison, an ordinary syringe with the attachment of a spray nozzle showed almost 90% viable cells post transplantation and provided an equally good distribution of the cell suspension.We also studied different silver containing dressings regarding silver accumulation in human skin. In addition, we graded the re-epithelialization to evaluate whether the dressings caused any delay in the wound healing process. We found that the silver dressings tested, with few exceptions, caused dermal accumulation of silver, primarily aggregated around blood vessels. We could also show that most of the dressings had negative effect on the re-epithelialization.For the restoration of the dermal layer of the skin, Integra® DRT functions as a scaffold for guided tissue regeneration of the dermis. We had the possibility to study a case of necrotizing fasciitis were the treatment consisted of the use of Integra® DTR together with sub-atmospheric pressure (after initial surgical debridement) and later transplantation of split thickness skin grafts. This measure proved to be safe as well as giving satisfactory pliable and aesthetically acceptable result.
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| 5. |
- Wallin, Åsa, 1976-
(författare)
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Molecular Studies of Irradiation and SN-38 on Colorectal Cancer
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Colorectal cancer (CRC) is one of most common cancer diseases worldwide. In Swedenapproximately 5,000 new cases of CRC are generated each year, which makes it the thirdmost common cancer disease among both men and women. The past decades ofimproved treatment strategies have considerably increased the five-year survival for CRCpatients. However more could be achieved in this area, in particular for metastatic CRC,which is the cause of most CRC-related deaths. Therefore it is important to study thebiological response to certain treatments induced in CRC to find valuable predictiveand/or prognostic factors to select patients for better suited treatments.The aim of this thesis was to gain insight into the molecular changes that occurfollowing irradiation or treatment with SN-38 in rectal cancer patients or colon cancercell lines by studying the RNA expression, protein expression, DNA cell cycledistribution and apoptotic response. The expression of phosphatase of regenerating liver(PRL) proteins was investigated in rectal cancers from 125 patients included in arandomized clinical trial of preoperative radiotherapy (RT). Increased expression of PRLswas seen at the invasive margin of primary and metastatic cancers compared with theinner area of the tumors. Moreover, strong PRL staining at the invasive margin correlatedto distant recurrence and worse survival of patients in the RT group but not in non-RTgroup (Paper I). Radiosensitivity was studied by treating KM12C, KM12SM andKM12L4a colon cancer cell lines with radiation. KM12C is of low metastatic naturecompared with the highly metastatic KM12SM and KM12L4a. Upregulation of ΔNp73and PRL-3 might contribute to the radioresistant phenotype in KM12C. In contrast,KM12L4a shows a high frequency of apoptosis and lack of upregulation of ΔNp73, PRL-3 and survivin, which might explain its radiosensitive phenotype (Paper II). KM12C,KM12SM and KM12L4a were treated with SN-38 which inhibits topoisomerase 1 (topo-1). The results show that SN-38 induces G2/S arrest and possess the capacity to triggerapoptosis in the three cell lines (Paper III). To further elucidate SN-38 effect on these celllines, the gene expression profile following SN-38 treatment was studied. Oligonucleotidearrays consisting of ~27,000 spots were hybridized with sample and reference cDNA.Both unsupervised and supervised hierarchical clustering analysis, and functional analysiswere performed. Supervised hierarchical clustering gives a strong signal of 1453discriminated genes, the vast majority being upregulated. Both upregulated anddownregulated genes point toward a favorable impact of SN-38 regarding the apoptoticpathways. For example RhoB and Bax are upregulated together with downregulation ofKras and survivin, which promotes apoptosis (Paper IV).In conclusion, PRLs may be valuable biomarkers for RT resistance, predicting apoor prognosis in rectal cancer patients. Targeting radio-resistance factors, such asΔNp73 and survivin may contribute to an increased sensitivity to RT. SN-38 affects cellproliferation and apoptosis.
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| 7. |
- Kotti, Angeliki
(författare)
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Clinical and Biological Factors Related to Survival in Patients with Rectal Cancer
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Rectal cancer is a common malignancy within the gastrointestinal tract. Despite the advances in diagnosis and treatment of rectal cancer patients during the last decades, there are still many patients who die from their disease. In order to personalise the therapy and optimise the clinical outcomes, it is important to identify factors that have an impact on survival of rectal cancer patients. Therefore, the overall aim of this thesis was to identify clinical and biological factors that were related to survival in patients with rectal cancer. Paper I aimed to evaluate the impact of statins on survival in older and younger patients with rectal cancer. The study included 238 older patients (≥70 years) and 227 younger patients (<70 years) from the southeast healthcare region of Sweden. The patients were classified as statin users if they used any type of statins at the time of the cancer diagnosis. In the older group, statin users had better cancer-specific survival, disease-free survival, and overall survival compared with non-users. No such association was present in the younger group. Paper II aimed to evaluate the impact of computed tomography (CT)-measured body composition on survival in rectal cancer patients. The study included 173 patients from the region Ostergotland of Sweden who underwent a CT colonography at the time of diagnosis. Skeletal muscle index (SMI) and visceral adipose tissue area (VAT) were quantified at the level of the third lumbar vertebral body, using the CT colonography acquired at the time of diagnosis. The patients were divided into a low or high SMI group, and a low or high VAT group. Low SMI was related to worse survival compared to high SMI in all the patients. High VAT was related to better survival in men with low or middle rectal cancer, while high VAT was related to worse survival in women with low or middle rectal cancer. Paper III aimed to evaluate the prognostic value of SPARCL1 expression in patients with rectal cancer with a focus on radiotherapy (RT). The study included 138 patients with rectal cancer who participated in the Swedish Rectal Cancer Trial. Of those, 63 patients underwent both preoperative RT and surgery, while 75 patients had surgery alone. SPARCL1 expression was determined by immunohistochemistry. Strong SPARCL1 expression was related to better overall survival compared to weak SPARCL1 expression in patients with stage III disease who received RT, but not in patients with stage III disease who did not receive RT. Moreover, SPARCL1 expression was increased in primary tumours with RT compared to tumours without RT. In summary, statin use was related to improved survival in older patients with rectal cancer. CT-measured body composition parameters provided useful information for determining the prognosis of rectal cancer patients. SPARCL1 was identified as a potential prognostic biomarker in rectal cancer patients who received preoperative RT. Conclusively, the results of this thesis indicate that statin drugs, CT-measured body composition and SPARCL1 are factors related to survival in patients with rectal cancer. The evidence may benefit patients by more accurate estimating of their prognosis, personalised treatment and improved clinical outcomes.
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| 8. |
- Lewander, Andreas, 1973-
(författare)
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Polymorphism and expression of NF-κB in relation to susceptibility and prognosis of colorectal cancer patients
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Normal human cells are strictly controlled in their environment by extrinsic and intrinsic factors. Despite this, some cells begin to develop into cancer cells, and if this process is allowed to continue, it will develop into cancer disease. To become cancerous, a cell must break several biological barriers. Two important barriers are apoptosis and cellular growth control.Cancer is a multifactorial disease caused by environmental and hereditary factors. The incidence of colorectal cancer varies among different populations around the world. Sweden has a history of a relatively high incidence of colorectal cancer, whereas its incidence in China is relatively low.Nuclear factor kappa B (NF-κB) is a transcription factor protein family, regulating genes involved in several aspects of cancer development. In human cells five members have been identified: NFKB1 (p105/p50), NFKB2 (p100/p52), RelA (p65), RelB and c-Rel. They normally form homo- or heterodimers in the cytoplasm of the cells, where they are in an inactive state by binding to inhibitory proteins, I kappaB-α, -θ and -ε and Bcl-3. Stimulatory signals, both intrinsic and extrinsic, lead the inhibitory proteins to be phosphorylated, which marks them for degradation. On activation, NF-κB proteins are often posttranslationally modified.In the first project, we investigated the role of a polymorphism in the promoter region of NFKB1 gene. The polymorphism is a 4-basepair insertion/deletion located 94 basepairs upstream of the gene (-94ins/delATTG). It does not seem to alter the amino acid sequence of the protein and therefore does not alter the function of the protein itself. Instead, it alters the regulation of the protein transcription. The aim of the present study was to investigate whether the polymorphism was related to cancer risk or clinicopathological variables. We found that this polymorphism increased the risk of sporadic colorectal cancer in a Swedish population but not in Swedish populations with a family history of colorectal cancer or in Chinese population.In the second project we studied an 8-basepair insertion/deletion polymorphism in the promoter region of NFKBIA gene coding for the nuclear factor kappa B inhibitory protein, IκBα. This polymorphism is located 708 basepairs upstream of the gene (-708ins/del8). The aim of the study was to investigate whether the polymorphism was related to cancer risk or clinicopathological factors. We found that this polymorphism was very rare in a Swedish population of colorectal cancer patients and controls and was totally absent in a Chinese population of patients and controls. Our conclusion is that this polymorphism is too rare to have a major impact on colorectal cancer incidence in the two populations.In the third project we studied levels of p65 phosphorylated at Serine-536 in colorectal cancers in a Swedish population. After activation and IκB phosphorylation/degradation, p65 is phosphorylated at Serine-536. This phosphorylation is involved in regulating transcriptional activity, nuclear localisation and protein stability. The aim of the study was to investigate whether the expression of the phosphorylated protein correlated to any clinicopathological variables, including survival. The expression of p65 phosphorylated at Serine-536 increased from normal mucosa to primary tumour, but no further increase to lymph node metastases was found. We did find, however, that the strong expression in the cytoplasm was correlated to worse survival among the patients, independent of gender, age, tumour location, stage and differentiation.In the fourth project we continued to study p65 phosphorylated at Serine-536. In this project, however, we studied the expression in a population of rectal cancer patients who participated in a Swedish clinical trial of preoperative radiotherapy. The aim of the study was to investigate whether the expression correlated to response to radiotherapy or to clinicopathological and some biological factors. We found that the expression was increased from normal mucosa to primary tumour, but detected no further increase from primary tumour to lymph node metastases. We found that the expression of p65 protein phosphorylated at Serine-536 was positively related to expression of TEM1, FXYD-3, PRL, p73 and MAC30 in the group of patients who received radiotherapy. Although no such relationship was seen in the group of patients that had not received radiotherapy, we did not find that the expression of p65 protein phosphorylated at Serine-536 was directly related to the clinical response to radiotherapy.In summary, the -94ins/delATTG polymorphism in the promoter region of NFKB1 gene increases the risk of sporadic colorectal cancer in Swedish but not in Chinese populations. The -708ins/del8 polymorphism in the promoter region of the NFKBIA gene is too rare to have a major impact on colorectal cancer incidence in Swedish and Chinese populations. Strong expression of p65 protein phosphorylated at Serine-536 is independently related to worse survival in Swedish colorectal cancer patients, and the expression is positively correlated to biological factors associated with more malignant features of tumours in rectal cancer patients who received preoperative radiotherapy.
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| 9. |
- Loftås, Per, 1964-
(författare)
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Response to neoadjuvant treatment in rectal cancer surgery
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Rectal cancer is one of the three most common malignancies in Sweden with an annual incidence of about 2000 cases. Current treatment consists of surgical resection of the rectum including the loco-regional lymph nodes in the mesorectum. In advanced cases, neoadjuvant chemo-radiotherapy (CRT) prior to the operative treatment reduces local recurrences and enables surgery. The neoadjuvant treatment can also eradicate the tumour completely, i.e. complete response. This research project was designed to investigate the effects of preoperative radiotherapy/ CRT and analyze methods to predict response to CRT.Study I investigated the expression of the FXYD-3 protein with immunohistochemistry in rectal cancer, with or without preoperative radiotherapy. The results from the total cohort showed that, strong FXYD-3 expression was correlated to infiltrative tumour growth (p = 0.02). In the radiotherapy group, strong FXYD-3 expression was related to an unfavourable prognosis (p = 0.02). Tumours with strong FXYD-3 expression had less tumour necrosis (p = 0.02) after radiotherapy. FXYD-3 expression in the primary tumour was increased compared to normal mucosa (p=0.008). We concluded that FXYD-3 expression was a prognostic factor in patients receiving preoperative radiotherapy for rectal cancer.Study II investigated FXYD-3 expression in tumours that developed local recurrences following surgery and compared this with expression in tumours that did not develop local recurrences. There was no difference in the expression of FXYD-3 between the group that developed local recurrences and the group that did not develop local recurrences. There was no difference in survival between those with strong or weak FXYD-3 expression. We concluded that this study could not confirm the findings from study 1 i.e. that FXYD-3 expression has prognostic significance in rectal cancer.Study III was a register-based study on the incidence and effects of complete response to neoadjuvant treatment. Eight per cent of the patients with adequate CRT to achieve complete response also had a complete histological response of the luminal tumor in the resected bowel. Sixteen per cent of that group had remaining lymph node metastases in the operative specimen. Chemotherapy together with radiotherapy doubled the chance of complete response in the luminal tumour. Patients with remaining lymph node metastases had a lower survival rate compared to those without. We concluded that residual nodal involvement after neoadjuvant treatment was an important factor for reduced survival after complete response in the luminal tumour.Study IV followed up the results from the previous study by re-evaluating magnetic resonance imaging (MRI)- images in patients with complete tumour response. Two experienced MRI radiologists performed blinded re-staging of post CRT MR- images from patients with complete response in the luminal tumour. One group with lymph node metastases and another one without were studied and the results compared with the pathology reports. The sensitivity, specificity, and positive and negative predicted values for correct staging of positive lymph nodes was 37%, 84%, 70% and 57%. The size of the largest lymph node (4.5 mm, p=0.04) seemed to indicate presence of a tumour positive lymph node. We concluded that MRI couldn’t correctly stage patients for lymph node metastases in patients with complete response to CRT in the luminal tumour.
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| 10. |
- Luo, Yifei, et al.
(författare)
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Technology Roadmap for Flexible Sensors
- 2023
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Ingår i: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
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Forskningsöversikt (refereegranskat)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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