Pancreatic cancer is one of the most devastating solid tumors, and it remains one of the most difficult to treat. The treatment of metastatic pancreatic cancer (MPC) is systemic, based on chemotherapy or best supporti...Pancreatic cancer is one of the most devastating solid tumors, and it remains one of the most difficult to treat. The treatment of metastatic pancreatic cancer (MPC) is systemic, based on chemotherapy or best supportive care, depending on the performance status of the patient. Two chemotherapeutical regimens have produced substantial benefits in the treatment of MPC: gemcitabine in 1997; and FOLFIRIONOX in 2011. FOLFIRINOX improved the natural history of MPC, with overall survival (OS) of 11.1 mo. Nab-paclitaxel associated with gemcitabine is a newly approved regimen for MPC, with a median OS of 8.6 mo. Despite multiple trials, this targeted therapy was not efficient in the treatment of MPC. Many new molecules targeting the proliferation and survival pathways, immune response, oncofetal signaling and the epigenetic changes are currently undergoing phase I and II trials for the treatment of MPC, with many promising results.展开更多
Living objects have complex internal and external interactions. The complexity is regulated and controlled by homeostasis, which is the balance of multiple opposing influences. The environmental effects finally guide ...Living objects have complex internal and external interactions. The complexity is regulated and controlled by homeostasis, which is the balance of multiple opposing influences. The environmental effects finally guide the self-organized structure. The living systems are open, dynamic structures performing random, stationary, stochastic, self-organizing processes. The self-organizing procedure is defined by the spatial-temporal fractal structure, which is self-similar both in space and time. The system’s complexity appears in its energetics, which tries the most efficient use of the available energies;for that, it organizes various well-connected networks. The controller of environmental relations is the Darwinian selection on a long-time scale. The energetics optimize the healthy processes tuned to the highest efficacy and minimal loss (minimalization of the entropy production). The organism is built up by morphogenetic rules and develops various networks from the genetic level to the organism. The networks have intensive crosstalk and form a balance in the Nash equilibrium, which is the homeostatic state in healthy conditions. Homeostasis may be described as a Nash equilibrium, which ensures energy distribution in a “democratic” way regarding the functions of the parts in the complete system. Cancer radically changes the network system in the organism. Cancer is a network disease. Deviation from healthy networking appears at every level, from genetic (molecular) to cells, tissues, organs, and organisms. The strong proliferation of malignant tissue is the origin of most of the life-threatening processes. The weak side of cancer development is the change of complex information networking in the system, being vulnerable to immune attacks. Cancer cells are masters of adaptation and evade immune surveillance. This hiding process can be broken by electromagnetic nonionizing radiation, for which the malignant structure has no adaptation strategy. Our objective is to review the different sides of living complexity 展开更多
Multiple primary lung cancer(MPLC)is an increasingly prevalent subtype of lung cancer.According to recent genomic studies,the different lesions of a single MPLC patient exhibit functional similarities that may reflect...Multiple primary lung cancer(MPLC)is an increasingly prevalent subtype of lung cancer.According to recent genomic studies,the different lesions of a single MPLC patient exhibit functional similarities that may reflect evolutionary convergence.We perform whole-exome sequencing for a unique cohort of MPLC patients with multiple samples from each lesion found.Using our own and other relevant public data,evolutionary tree reconstruction reveals that cancer driver gene mutations occurred at the early trunk,indicating evolutionary contingency rather than adaptive convergence.Additionally,tumors from the same MPLC patient are as genetically diverse as those from different patients,while within-tumor genetic heterogeneity is significantly lower.Furthermore,the aberrant molecular functions enriched in mutated genes for a sample show a strong overlap with other samples from the same tumor,but not with samples from other tumors or other patients.Overall,there is no evidence of adaptive convergence during the evolution of MPLC.Most importantly,the similar between-tumor diversity and between-patient diversity suggest that personalized therapies may not adequately account for the genetic diversity among different tumors in an MPLC patient.To fully exploit the strategic value of precision medicine,targeted therapies should be designed and delivered on a per-lesion basis.展开更多
A computational analysis of genome-scale transcriptomic data collected on -1,700 tissue samples of three cancer types： breast carcinoma, colon adenocarcinoma and lung adenocarcinoma, revealed that each tissue consist...A computational analysis of genome-scale transcriptomic data collected on -1,700 tissue samples of three cancer types： breast carcinoma, colon adenocarcinoma and lung adenocarcinoma, revealed that each tissue consists of （at least） two major subpopulations of cancer cells with different capabilities to handle fluctuating Oz levels. The two populations have distinct genomic and transcriptomic characteristics, one accelerating its proliferation under hypoxic conditions and the other proliferating faster with higher O2 levels, referred to as the hypoxia and the reoxygenation subpopulations, respectively. The proportions of the two subpopulations within a cancer tissue change as the average 02 level changes. They both contribute to cancer development but in a complementary manner. The hypoxia subpopulation tends to have higher proliferation rates than the reoxygenation one as well as higher apoptosis rates; and it is largely responsible for the acidic environment that enables tissue invasion and provides protection against attacks from T-cells. In comparison, the reoxygenation subpopulation generates new extracellular matrices in support of further growth of the tumor and strengthens cell-cell adhesion to provide scaffolds to keep all the cells connected. This subpopulation also serves as the major source of growth factors for tissue growth. These data and observations strongly suggest that these two major subpopulations within each tumor work together in a conjugative relationship to allow the tumor to overcome stresses associated with the constantly changing Oz level due to repeated growth and angiogenesis. The analysis results not only reveal new insights about the population dynamics within a tumor but also have implications to our understanding of possible causes of different cancer phenotypes such as diffused versus more tightly connected tumor tissues.展开更多
The objective was to gain proof of genome damage-repair induced mitotic slippage process (MSP) to 4n-diplochromosome skewed division-system, earlier suggested to have “cancer-deciding” consequences. Our damage-model...The objective was to gain proof of genome damage-repair induced mitotic slippage process (MSP) to 4n-diplochromosome skewed division-system, earlier suggested to have “cancer-deciding” consequences. Our damage-model showed two succeeding phases: molecular mutations for initiation of fitness-gained cells, and large chromosomal changes to aneuploidy from inherited DNA-breakage-repair inaccuracies. The mutations were gained while DNA-repair and DNA-replication, co-existed in the route to tetraploidy, a phenomenon also expressed for some existing unicellular organisms. These organisms also showed genome reductive, amitotic, meioticlike division, and was the origin of human genome conserved, self-inflicted 90° reorientation of the 4n nucleus relative to the cytoskeleton axis. In the in vitro DNA-damage model, this remarkable 4n-event deciding “flat-upright” cell-growth characteristics showed several consequences, for example, cancer-important, E-cadherin-β-catenin cell-to-cell adherence destruction, which gave diploid progeny cells, mobility freedom from cell contact inhibition, likely in renewal tissues. This 4n-skewed division-system with inheritance in progeny cells for repeat occurrences as mentioned for flat-up-right growth patterns is similar to claimed concepts of metaplasia-EMT/MET embryogenesis events in cancer evolution. A scrutiny of this literature, proof-wise invalidated this embryological concept by tetraploid 8C cells occurring in MET events and, was noted for small cell occurrence, i.e., diploidy from 4n-8C reductive division, an also event for tumor relapse cells, derived from genome damaging therapy agents. Pre-cancer hyperplasia reported MSP, cadherincatenin destruction and 90° perpendicularity to basal cell membrane. The DNA-damage-repair model can weed-out therapy-agents triggering 4n-skewed division. Cancer-control, beginning-information, is likely from mutational identity of the 4n derived fitness-gained cells.展开更多
With the progress and development of computer technology,applying machine learning methods to cancer research has become an important research field.To analyze the most recent research status and trends,main research ...With the progress and development of computer technology,applying machine learning methods to cancer research has become an important research field.To analyze the most recent research status and trends,main research topics,topic evolutions,research collaborations,and potential directions of this research field,this study conducts a bibliometric analysis on 6206 research articles worldwide collected from PubMed between 2011 and 2021 concerning cancer research using machine learning methods.Python is used as a tool for bibliometric analysis,Gephi is used for social network analysis,and the Latent Dirichlet Allocation model is used for topic modeling.The trend analysis of articles not only reflects the innovative research at the intersection of machine learning and cancer but also demonstrates its vigorous development and increasing impacts.In terms of journals,Nature Communications is the most influential journal and Scientific Reports is the most prolific one.The United States and Harvard University have contributed the most to cancer research using machine learning methods.As for the research topic,“Support Vector Machine,”“classification,”and“deep learning”have been the core focuses of the research field.Findings are helpful for scholars and related practitioners to better understand the development status and trends of cancer research using machine learning methods,as well as to have a deeper understanding of research hotspots.展开更多
Lung cancer is one of the leading causes of all cancer-related deaths. Circulating tumor DNA (ctDNA) is released from apoptotic and necrotic tumor cells. Several sensitive techniques have been invented and adapted to ...Lung cancer is one of the leading causes of all cancer-related deaths. Circulating tumor DNA (ctDNA) is released from apoptotic and necrotic tumor cells. Several sensitive techniques have been invented and adapted to quantify ctDNA genomic alterations. Applications of ctDNA in lung cancer include early diagnosis and detection, prognosis prediction, detecting mutations and structural alterations, minimal residual disease, tumor mutational burden, and tumor evolution tracking. Compared to surgical biopsy and radiographic imaging, the advantages of ctDNA are that it is a non-invasive procedure, allows real-time monitoring, and has relatively high sensitivity and specificity. Given the massive research on non-small cell lung cancer, attention should be paid to small cell lung cancer.展开更多
The entropy production rate was determined for avascular tumor growth. The proposed formula relates the fractal dimension of the tumor contour with the quotient between mitosis and apoptosis rate, which can be used to...The entropy production rate was determined for avascular tumor growth. The proposed formula relates the fractal dimension of the tumor contour with the quotient between mitosis and apoptosis rate, which can be used to characterize the degree of proliferation of tumor cells. The entropy production rate was determined for fourteen tumor cell lines as a physical function of cancer robustness. The entropy production rate is a hallmark that allows us the possibility of prognosis of tumor proliferation and invasion capacities, key fac-tors to improve cancer therapy.展开更多
Human papillomavirus 58 (HPV58) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV58 has been reported in Asia, Africa and some other areas. However, due to the scattered di...Human papillomavirus 58 (HPV58) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV58 has been reported in Asia, Africa and some other areas. However, due to the scattered distribution of global data, in addition to the lack of data of some HPV58 high-incidence nations and regions, like China's Mainland, a comprehensive analysis of the global geographical distribution of HPV58 remains blank so far. In this study, HPV58 from the human cervical cancer tissue was detected in China's Mainland, and 14 new HPV58-E6/L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV58 sequences that have been deposited in GenBank since 1985. The study result shows that the sequences detected from the Shanghai, Jiangsu and Sichuan areas are homologous with those found in the past from Hong Kong and Xi'an, China, as well as Japan and other Southeast Asian areas. Furthermore, Western Africa is considered to be the "root" source of the HPV58 variant, while China's Mainland and Southeast Asia are "transit points" and the new sources of HPV58 after receiving the isolates from the "root" source; like HPV16 and HPV18, the HPV58 might also be one of the major HPV types associated with the development and spread of cervical cancer.展开更多
文摘Pancreatic cancer is one of the most devastating solid tumors, and it remains one of the most difficult to treat. The treatment of metastatic pancreatic cancer (MPC) is systemic, based on chemotherapy or best supportive care, depending on the performance status of the patient. Two chemotherapeutical regimens have produced substantial benefits in the treatment of MPC: gemcitabine in 1997; and FOLFIRIONOX in 2011. FOLFIRINOX improved the natural history of MPC, with overall survival (OS) of 11.1 mo. Nab-paclitaxel associated with gemcitabine is a newly approved regimen for MPC, with a median OS of 8.6 mo. Despite multiple trials, this targeted therapy was not efficient in the treatment of MPC. Many new molecules targeting the proliferation and survival pathways, immune response, oncofetal signaling and the epigenetic changes are currently undergoing phase I and II trials for the treatment of MPC, with many promising results.
文摘Living objects have complex internal and external interactions. The complexity is regulated and controlled by homeostasis, which is the balance of multiple opposing influences. The environmental effects finally guide the self-organized structure. The living systems are open, dynamic structures performing random, stationary, stochastic, self-organizing processes. The self-organizing procedure is defined by the spatial-temporal fractal structure, which is self-similar both in space and time. The system’s complexity appears in its energetics, which tries the most efficient use of the available energies;for that, it organizes various well-connected networks. The controller of environmental relations is the Darwinian selection on a long-time scale. The energetics optimize the healthy processes tuned to the highest efficacy and minimal loss (minimalization of the entropy production). The organism is built up by morphogenetic rules and develops various networks from the genetic level to the organism. The networks have intensive crosstalk and form a balance in the Nash equilibrium, which is the homeostatic state in healthy conditions. Homeostasis may be described as a Nash equilibrium, which ensures energy distribution in a “democratic” way regarding the functions of the parts in the complete system. Cancer radically changes the network system in the organism. Cancer is a network disease. Deviation from healthy networking appears at every level, from genetic (molecular) to cells, tissues, organs, and organisms. The strong proliferation of malignant tissue is the origin of most of the life-threatening processes. The weak side of cancer development is the change of complex information networking in the system, being vulnerable to immune attacks. Cancer cells are masters of adaptation and evade immune surveillance. This hiding process can be broken by electromagnetic nonionizing radiation, for which the malignant structure has no adaptation strategy. Our objective is to review the different sides of living complexity
基金supported by the National Key Research and Development Program of China to J.-R. Y.(2021YFF1200904 and2021YFA1302500)the National Natural Science Foundation of China to J.-R. Y.(31871320 and 81830103)+1 种基金by Science and Technology Planning Project of ZhuHai,China to H. C.by Science and Technology Planning Project of Guangdong Province,China to X. Z.(2014A030304053)
文摘Multiple primary lung cancer(MPLC)is an increasingly prevalent subtype of lung cancer.According to recent genomic studies,the different lesions of a single MPLC patient exhibit functional similarities that may reflect evolutionary convergence.We perform whole-exome sequencing for a unique cohort of MPLC patients with multiple samples from each lesion found.Using our own and other relevant public data,evolutionary tree reconstruction reveals that cancer driver gene mutations occurred at the early trunk,indicating evolutionary contingency rather than adaptive convergence.Additionally,tumors from the same MPLC patient are as genetically diverse as those from different patients,while within-tumor genetic heterogeneity is significantly lower.Furthermore,the aberrant molecular functions enriched in mutated genes for a sample show a strong overlap with other samples from the same tumor,but not with samples from other tumors or other patients.Overall,there is no evidence of adaptive convergence during the evolution of MPLC.Most importantly,the similar between-tumor diversity and between-patient diversity suggest that personalized therapies may not adequately account for the genetic diversity among different tumors in an MPLC patient.To fully exploit the strategic value of precision medicine,targeted therapies should be designed and delivered on a per-lesion basis.
文摘A computational analysis of genome-scale transcriptomic data collected on -1,700 tissue samples of three cancer types： breast carcinoma, colon adenocarcinoma and lung adenocarcinoma, revealed that each tissue consists of （at least） two major subpopulations of cancer cells with different capabilities to handle fluctuating Oz levels. The two populations have distinct genomic and transcriptomic characteristics, one accelerating its proliferation under hypoxic conditions and the other proliferating faster with higher O2 levels, referred to as the hypoxia and the reoxygenation subpopulations, respectively. The proportions of the two subpopulations within a cancer tissue change as the average 02 level changes. They both contribute to cancer development but in a complementary manner. The hypoxia subpopulation tends to have higher proliferation rates than the reoxygenation one as well as higher apoptosis rates; and it is largely responsible for the acidic environment that enables tissue invasion and provides protection against attacks from T-cells. In comparison, the reoxygenation subpopulation generates new extracellular matrices in support of further growth of the tumor and strengthens cell-cell adhesion to provide scaffolds to keep all the cells connected. This subpopulation also serves as the major source of growth factors for tissue growth. These data and observations strongly suggest that these two major subpopulations within each tumor work together in a conjugative relationship to allow the tumor to overcome stresses associated with the constantly changing Oz level due to repeated growth and angiogenesis. The analysis results not only reveal new insights about the population dynamics within a tumor but also have implications to our understanding of possible causes of different cancer phenotypes such as diffused versus more tightly connected tumor tissues.
文摘The objective was to gain proof of genome damage-repair induced mitotic slippage process (MSP) to 4n-diplochromosome skewed division-system, earlier suggested to have “cancer-deciding” consequences. Our damage-model showed two succeeding phases: molecular mutations for initiation of fitness-gained cells, and large chromosomal changes to aneuploidy from inherited DNA-breakage-repair inaccuracies. The mutations were gained while DNA-repair and DNA-replication, co-existed in the route to tetraploidy, a phenomenon also expressed for some existing unicellular organisms. These organisms also showed genome reductive, amitotic, meioticlike division, and was the origin of human genome conserved, self-inflicted 90° reorientation of the 4n nucleus relative to the cytoskeleton axis. In the in vitro DNA-damage model, this remarkable 4n-event deciding “flat-upright” cell-growth characteristics showed several consequences, for example, cancer-important, E-cadherin-β-catenin cell-to-cell adherence destruction, which gave diploid progeny cells, mobility freedom from cell contact inhibition, likely in renewal tissues. This 4n-skewed division-system with inheritance in progeny cells for repeat occurrences as mentioned for flat-up-right growth patterns is similar to claimed concepts of metaplasia-EMT/MET embryogenesis events in cancer evolution. A scrutiny of this literature, proof-wise invalidated this embryological concept by tetraploid 8C cells occurring in MET events and, was noted for small cell occurrence, i.e., diploidy from 4n-8C reductive division, an also event for tumor relapse cells, derived from genome damaging therapy agents. Pre-cancer hyperplasia reported MSP, cadherincatenin destruction and 90° perpendicularity to basal cell membrane. The DNA-damage-repair model can weed-out therapy-agents triggering 4n-skewed division. Cancer-control, beginning-information, is likely from mutational identity of the 4n derived fitness-gained cells.
基金Natural Science Foundation of Guangdong Province,Grant/Award Number:2021A1515011339。
文摘With the progress and development of computer technology,applying machine learning methods to cancer research has become an important research field.To analyze the most recent research status and trends,main research topics,topic evolutions,research collaborations,and potential directions of this research field,this study conducts a bibliometric analysis on 6206 research articles worldwide collected from PubMed between 2011 and 2021 concerning cancer research using machine learning methods.Python is used as a tool for bibliometric analysis,Gephi is used for social network analysis,and the Latent Dirichlet Allocation model is used for topic modeling.The trend analysis of articles not only reflects the innovative research at the intersection of machine learning and cancer but also demonstrates its vigorous development and increasing impacts.In terms of journals,Nature Communications is the most influential journal and Scientific Reports is the most prolific one.The United States and Harvard University have contributed the most to cancer research using machine learning methods.As for the research topic,“Support Vector Machine,”“classification,”and“deep learning”have been the core focuses of the research field.Findings are helpful for scholars and related practitioners to better understand the development status and trends of cancer research using machine learning methods,as well as to have a deeper understanding of research hotspots.
基金grants from the Intergovernmental International Science,Technology and Innovation Cooperation Key Project of the National Key R&D Programme(NKP)(No.2017YFE0110300)the National Natural Science Foundation of China(No.81602162)the Chinese Academy of Medical Sciences(CAMS)Initiative for Innovative Medicine(CAMS-I2M)(No.2016-I2M-1-002).
文摘Lung cancer is one of the leading causes of all cancer-related deaths. Circulating tumor DNA (ctDNA) is released from apoptotic and necrotic tumor cells. Several sensitive techniques have been invented and adapted to quantify ctDNA genomic alterations. Applications of ctDNA in lung cancer include early diagnosis and detection, prognosis prediction, detecting mutations and structural alterations, minimal residual disease, tumor mutational burden, and tumor evolution tracking. Compared to surgical biopsy and radiographic imaging, the advantages of ctDNA are that it is a non-invasive procedure, allows real-time monitoring, and has relatively high sensitivity and specificity. Given the massive research on non-small cell lung cancer, attention should be paid to small cell lung cancer.
文摘The entropy production rate was determined for avascular tumor growth. The proposed formula relates the fractal dimension of the tumor contour with the quotient between mitosis and apoptosis rate, which can be used to characterize the degree of proliferation of tumor cells. The entropy production rate was determined for fourteen tumor cell lines as a physical function of cancer robustness. The entropy production rate is a hallmark that allows us the possibility of prognosis of tumor proliferation and invasion capacities, key fac-tors to improve cancer therapy.
基金Supported by the National Science and Technology Pillar Program of China (Grant No. 2007BAI24B01)the National High Technology Research and Development Program of China (Grant No. 2006AA02Z342)the Shanghai Leading Academic Discipline Project (B111) and Shanghai Science and Technology Committee (Grant No. 07XD14025)
文摘Human papillomavirus 58 (HPV58) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV58 has been reported in Asia, Africa and some other areas. However, due to the scattered distribution of global data, in addition to the lack of data of some HPV58 high-incidence nations and regions, like China's Mainland, a comprehensive analysis of the global geographical distribution of HPV58 remains blank so far. In this study, HPV58 from the human cervical cancer tissue was detected in China's Mainland, and 14 new HPV58-E6/L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV58 sequences that have been deposited in GenBank since 1985. The study result shows that the sequences detected from the Shanghai, Jiangsu and Sichuan areas are homologous with those found in the past from Hong Kong and Xi'an, China, as well as Japan and other Southeast Asian areas. Furthermore, Western Africa is considered to be the "root" source of the HPV58 variant, while China's Mainland and Southeast Asia are "transit points" and the new sources of HPV58 after receiving the isolates from the "root" source; like HPV16 and HPV18, the HPV58 might also be one of the major HPV types associated with the development and spread of cervical cancer.
