Cell signaling refers to the mechanisms by which cells communicate with each other to coordinate various functions. There are five main types of cell signaling based on the distance between the signaling and target cells: Autocrine Signaling • Definition: The cell releases signaling molecules that bind to receptors on its own surface. • Function: Common in immune responses and cell growth regulation. • Example: T-cells producing and responding to interleukin-2 (IL-2). Paracrine Signaling • Definition: Signals are released by a cell and affect nearby target cells. • Function: Used in local communication between cells, such as in tissue repair. • Example: Neurotransmitters released at synapses or growth factors acting in wound healing. Endocrine Signaling • Definition: Hormones are secreted into the bloodstream and travel to distant target cells. • Function: Regulates long-distance communication in the body. • Example: Insulin released by the pancreas affecting glucose uptake in muscles and liver. Juxtacrine Signaling (Contact-Dependent) • Definition: Cells communicate through direct contact, often via membrane-bound molecules. • Function: Important in immune responses and development. • Example: Interaction between antigen-presenting cells and T-cells via MHC molecules. Intracine Signaling • Definition: Intracrine signaling (or intracrine signalling) refers to a type of cell signaling in which a hormone or signaling molecule acts within the same cell that produced it, without ever being secreted into the extracellular space. • Function: It triggers responses like gene expression or metabolic changes directly in the producing cell. • Example: Steroid Hormones (e.g., estrogen, testosterone) can act intracrinally by binding to intracellular receptors within the cell that synthesized them, altering gene expression.

Arthropods are the largest and most diverse phylum in the animal kingdom, encompassing millions of species—from insects and spiders to crabs and centipedes. Found in nearly every environment on Earth, arthropods play vital roles in ecosystems, agriculture, and even human health. But what exactly makes an animal an arthropod? Here are the defining characteristics that set them apart: Exoskeleton Made of Chitin Arthropods have a tough, external skeleton called an exoskeleton, made primarily of chitin. This protective armor shields them from predators, prevents water loss, and supports muscle attachment. However, since it doesn’t grow with the animal, arthropods must periodically molt (shed) their exoskeleton in a process called ecdysis. Segmented Body Their bodies are typically divided into segments, often organized into three main regions: • Head – where sensory organs and mouthparts are located • Thorax – the center of locomotion, bearing legs and wings (in insects) • Abdomen – where digestion, reproduction, and other internal processes occur Some groups, like spiders, have different segment arrangements, but segmentation remains a consistent feature across the phylum. Jointed Appendages As their name implies (arthro = joint, pod = foot), arthropods have jointed limbs. These flexible appendages allow for complex movement and are adapted for various functions—walking, swimming, flying, sensing, feeding, and defense. Bilateral Symmetry Arthropods have bilateral symmetry, meaning their body can be divided into two mirror-image halves. This symmetry aids in balance, directional movement, and coordination. Open Circulatory System Instead of a closed circulatory system like humans, arthropods pump hemolymph (a fluid analogous to blood) into body cavities, where it bathes organs directly. This open circulatory system is less efficient but well-suited to their relatively small body size and energy needs. Ventral Nerve Cord and Dorsal Brain Arthropods possess a centralized nervous system consisting of a brain and a ventral nerve cord. Ganglia (clusters of neurons) control local body segments, allowing fast and efficient responses to stimuli. Diverse Sensory Organs Arthropods are equipped with a range of sophisticated sensory organs: • Compound eyes for detecting movement and color • Antennae for touch and smell • Setae (bristles) on their body for detecting vibrations and chemicals Incredible Diversity and Adaptability Arthropods have adapted to virtually every environment—deep oceans, mountaintops, deserts, rainforests, and even human homes. Their diversity includes: • Insects (e.g., bees, ants, butterflies) • Arachnids (e.g., spiders, scorpions, ticks) • Crustaceans (e.g., crabs, shrimp, lobsters) • Myriapods (e.g., centipedes, millipedes)

The five major similarities of Porifera are: 1. Porous structure 2. Filter feeding 3. Asexual reproduction 4. Cellular specialization 5. Aquatic habitat Specialized cells of Porifera and their functions: • Choanocytes : Absorb nutrients • Pinacocytes : Provide shape • Amoebocytes : Perform various tasks • Porocytes : Form pores (ostia) • Sclerocytes : Secrete spicules • Myocytes : Aid in movement Spicules are made of silica or calcium carbonate. The various tasks of Amoebocytes: • Distribute nutrient • Secrete the skeleton • Help in regeneration of tissue Choanocytes absorb nutrients through a process called intracellular digestion. Choanocytes, with their flagellum and collar of microvilli, create water currents that draw water and small food particles into the sponge. Choanocytes are called the digestive system of the sponges. Pinacocytes are flat cells that line the outer surface and canals, creating the pinacoderm. There are 3 types of pinacocytes: 1. Basipinacocytes → attached surface 2. Exopinacocytes → surface 3. Endopinacocytes → canal 3 main functions of amoebocytes: 1. Nutrient transportation 2. Gamete production 3. Sperm delivery There are more functions. They have pseudopodia, limb-like protein extensions that protrude out from the cell cytoplasm. Amoebocytes interact with other cells called trophocytes to form both the egg and sperm. Sponges use tiny pores (ostia) to draw water, oxygen, and food particles. Larger opening (oscula) expel water and waste products. Two types of Sclerocytes: 1. Calcoblast → Calcium carbonate 2. Silicoblast → Silic-based Myocytes are like the muscle cells.

What are Ribosomes? • A ribosome is a complex molecular machine found inside the living cells that produce proteins from amino acids during a process called protein synthesis or translation. The process of protein synthesis is a primary function, which is performed by all living cells. • Ribosomes are specialized cell organelles and are found in both prokaryotic and eukaryotic cells. Every living cell requires ribosomes for the production of proteins. • This cell organelle also functions by binding to a messenger ribonucleic acid (mRNA) and decoding the information carried by the nucleotide sequence of the mRNA. They transfer RNAs (tRNAs) comprising amino acids and enter into the ribosome at the acceptor site. Once it gets bound up, it adds amino acid to the growing protein chain on tRNA. Ribosomes Structure • A ribosome is a complex of RNA and protein and is, therefore, known as a ribonucleoprotein. It is composed of two subunits – smaller and larger. • The smaller subunit is where the mRNA binds and is decoded, and in the larger subunit, the amino acids get added. Both of the subunits contain both protein and ribonucleic acid components. • The two subunits are joined to each other by interactions between the rRNAs in one subunit and proteins in the other subunit. Ribosomes are located inside the cytosol found in the plant cell and animal cells. The ribosome structure includes the following: • It is located in two areas of cytoplasm. • Scattered in the cytoplasm. • Prokaryotes have 70S ribosomes while eukaryotes have 80S ribosomes. • Around 62% of ribosomes are comprised of RNA, while the rest is proteins. • The structure of free and bound ribosomes is similar and is associated with protein synthesis. Ribosomes Function The important ribosome function includes: 1. It assembles amino acids to form proteins that are essential to carry out cellular functions. 2. The DNA produces mRNA by the process of DNA transcription. 3. The mRNA is synthesized in the nucleus and transported to the cytoplasm for the process of protein synthesis. 4. The ribosomal subunits in the cytoplasm are bound around mRNA polymers. The tRNA then synthesizes proteins. 5. Ribosomes are the site of protein synthesis. 6. The proteins synthesized in the cytoplasm are utilized in the cytoplasm itself, the proteins synthesized by bound ribosomes are transported outside the cell.

Nuclear pores are protein-lined channels in the nuclear envelope that facilitate the bidirectional transport of molecules, including proteins and RNA, between the nucleus and the cytoplasm of eukaryotic cells. They act as selective gates, allowing small molecules and ions to pass freely while requiring specific signals for the movement of larger molecules.  Here's a more detailed breakdown: • Location : Nuclear pores are found in the nuclear envelope, a double membrane that surrounds the nucleus.  • Composition : Each nuclear pore is a large complex of proteins called the nuclear pore complex (NPC).  • Function: • Selective Transport: They allow the passage of small molecules and ions through the nuclear membrane.  • Active Transport: They mediate the active and efficient transport of larger molecules like proteins and RNA.  • Regulation: They regulate the flow of molecules between the nucleus and cytoplasm, ensuring the proper functioning of the cell.  • Signaling : Proteins destined for the nucleus carry a nuclear localization signal (NLS), which is recognized by the pore. Similarly, RNA and proteins leaving the nucleus have nuclear export sequences (NES).  • Structure : The NPC is a complex structure, composed of various proteins called nucleoporins, with a diameter of about 120 nm.  • Importance : Nuclear pores play a critical role in cell biology, controlling the exchange of molecules between the nucleus and cytoplasm. They are essential for maintaining proper cellular function and structure.

Golgi Apparatus Golgi Apparatus: The Packaging and Shipping Center of the Cell The Golgi Apparatus, also known as the Golgi Complex or Golgi Body, is a vital organelle found in eukaryotic cells. It plays a key role in modifying, sorting, packaging, and transporting proteins and lipids that are produced in the endoplasmic reticulum (ER). Structure of the Golgi Apparatus • The Golgi Apparatus looks like a stack of flattened, membrane-bound sacs called cisternae. • These stacks are often curved and arranged like a stack of pancakes. • It has two faces: • The cis face (receiving side) – located near the ER, where it receives newly made proteins and lipids. • The trans face (shipping side) – where modified substances are packaged and sent to their destinations. Functions of the Golgi Apparatus 1. Modification of Proteins and Lipids • Proteins and lipids from the ER are often not ready to be used immediately. The Golgi modifies them by adding sugars or other molecules to form glycoproteins and glycolipids. 2. Sorting and Packaging • Once modified, the Golgi sorts these substances based on their destination (inside the cell or outside). • It then packages them into small membrane-bound sacs called vesicles. 3. Transport • The vesicles carry proteins and lipids to where they are needed, including: • The plasma membrane (for secretion) • Lysosomes • Other parts of the cell 4. Production of Lysosomes • The Golgi also helps in forming lysosomes, which are small organelles that digest waste materials and worn-out cell parts. Why is the Golgi Apparatus Important? The Golgi Apparatus is like the post office or warehouse of the cell. Just like a postal system receives, processes, and delivers packages, the Golgi receives products from the ER, processes them, and sends them to the right location. Without the Golgi Apparatus: • Proteins and lipids would not be properly processed or sent to their correct destinations. • The cell would not be able to function efficiently or respond to its environment. Summary • Location: Near the endoplasmic reticulum • Structure: Stack of flattened sacs (cisternae) • Main roles: Modification, packaging, and transportation of proteins and lipids • Nicknames: Cell’s post office, packaging center, shipping station

Introduction The Endoplasmic Reticulum (ER): The Transport and Manufacturing System of the Cell The Endoplasmic Reticulum (ER) is one of the most important organelles found in eukaryotic cells (cells with a nucleus). It is a large network of flattened sacs and tubules that extends throughout the cytoplasm. The ER plays a major role in the production, processing, and transport of proteins and lipids that the cell needs to function. Types of Endoplasmic Reticulum There are two types of ER, each with its own structure and function: 1. Rough Endoplasmic Reticulum (RER): • The surface of the Rough ER is studded with ribosomes, which gives it a rough or grainy appearance under a microscope. • These ribosomes are the sites where proteins are synthesized. • The RER is especially abundant in cells that produce large amounts of protein, such as cells in the pancreas (which makes enzymes). • Once proteins are made by the ribosomes, the Rough ER helps fold, modify, and transport them to other parts of the cell or out of the cell through the Golgi apparatus. 2. Smooth Endoplasmic Reticulum (SER): • Unlike the Rough ER, the Smooth ER does not have ribosomes on its surface, making it appear smooth. • The SER is involved in the synthesis of lipids (fats), steroid hormones, and also plays a role in detoxifying chemicals and drugs in liver cells. • It also helps store calcium ions in muscle cells, which is important for muscle contraction. Functions of the Endoplasmic Reticulum The ER performs several essential functions in the cell: 1. Protein synthesis and processing (Rough ER) 2. Lipid and steroid synthesis (Smooth ER) 3. Detoxification of harmful substances (Smooth ER) 4. Transport of materials within the cell 5. Storage of calcium ions (especially in muscle cells) 6. Formation of vesicles that transport substances to the Golgi apparatus Importance of the ER in the Cell The Endoplasmic Reticulum is like the factory and highway system of the cell. It not only manufactures essential molecules but also ensures they are sent to the correct destination. Without the ER, cells would not be able to produce proteins and lipids efficiently, nor would they be able to properly process or transport them. It is essential for maintaining the structure, function, and overall health of the cell.

Heat is a form of energy. When something is hot, it means its particles (atoms or molecules) are moving around really fast. When it’s cold, the particles move slowly. 🔄 So What is Conduction Again? Conduction is the way heat energy moves through a solid. It happens when hot, fast-moving particles transfer their energy to cooler, slower ones by bumping into them—kind of like passing a secret through whispers! 🗣️➡️👂➡️👂 🧱 Why Solids? • In solids, particles are tightly packed together. • This makes it easy for one particle to bump into the next and pass on heat. • In liquids or gases, the particles are farther apart, so heat doesn’t move as quickly. 🥇 Best Conductors: Some materials let heat travel through them really well. These are called conductors. • 🔩 Metals like copper, aluminium, and iron are great conductors. • That’s why cooking pans, wires, and even kettles are made of metal. 🧤 Poor Conductors = Insulators Some materials are bad at letting heat through. These are called insulators. • Examples: wood, plastic, rubber, cloth, air. • That’s why: • Oven mitts are made of cloth. • We use wooden spoons in hot soup. • Thermos bottles have air layers inside to trap heat. 🔬 Particle-Level View (Imagine This): 1. 🔥 Heat is added to one end of a metal rod. 2. ⚡ Particles at the hot end start vibrating really fast. 3. 💥 These fast particles bump into nearby particles, making them vibrate faster. 4. 📈 This continues until the whole rod is warmer! 📚 Real-Life Examples of Conduction: • Holding a spoon in hot tea → handle gets warm. • Touching a hot doorknob on a sunny day. • Ironing clothes: the iron's heat transfers to the fabric.

Introduction • Nucleus, A membrane bound organelle in most of the Eukaryotic Cells, is a storage of genetic information and chromosome. Nucleus does not exist in some Eukaryotic Cells, like RBC and it exists more that 1 in some other Eukaryotic Cells, like Osteoclasts. • The nucleus in a cell performs three primary functions: 1) storing the cell's genetic information (DNA), 2) regulating gene expression through transcription, and 3) copying DNA during replication.  • Here's a more detailed explanation: 1. 1. Storing DNA : The nucleus houses the cell's DNA, which is organized into chromosomes and contains the instructions for cell growth, development, and reproduction, as well as directing protein synthesis.  2. 2. Regulating Gene Expression: The nucleus controls which genes are turned on or off, determining which proteins are produced. This process, called transcription, involves copying DNA into RNA, which then leaves the nucleus to guide protein synthesis in the cytoplasm.  3. 3. DNA Replication: The nucleus is also the site where DNA is duplicated during cell division, ensuring that each new daughter cell receives a complete set of genetic instructions.  Structure • In mammalian cells, the average diameter of the nucleus is approximately 6 mm, which occupies about 10% of the total cell volume. • 5 Major Parts of a Nucleus : 1. Nuclear Envelope: This double-layered membrane encloses the nucleus and separates it from the cytoplasm. It's continuous with the endoplasmic reticulum and contains nuclear pores that regulate the movement of molecules in and out of the nucleus.  2. Nuclear Lamina: This protein meshwork, located beneath the inner nuclear membrane, provides structural support and helps maintain the shape of the nucleus.  3. Nucleolus: This is a spherical body within the nucleus responsible for producing ribosomes, which are essential for protein synthesis.  4. Chromatin: This is the DNA and protein complex that makes up the chromosomes. During cell division, chromatin condenses into visible chromosomes.  5. Nucleoplasm: This is the gel-like substance within the nucleus that suspends the other nuclear components, including the nucleolus and chromatin.

#CellAdvanced Introduction • Cytoplasm is the jelly-like and semi-fluid structure present in the space between the cell membrane and nucleus. • 3 Main Functions of the Cytoplasm : 1. Structural Support and Cell Shape : The cytoplasm, along with the cytoskeleton, helps maintain the cell's shape and provides a framework for organelles to function properly.  2. Medium for Cellular Processes : The cytoplasm is where many important cellular activities, like protein synthesis, glycolysis, and cell division, take place.  3. Material Transport : Cytoplasmic streaming, a process where the cytoplasm moves around, helps transport nutrients, enzymes, and other substances within the cell, ensuring efficient distribution of resources.  Structure • The cytoplasm is often described as a viscous, jelly-like material. It's not entirely fluid, but rather has a consistency that allows for the movement of molecules and organelles. • The cytoplasm can change from a more fluid state (sol) to a thicker, more gel-like state (gel), depending on the cell's needs. • The three main parts of the cytoplasm are cytosol, organelles, and cytoplasmic inclusions. • The main component of the cytosol is water which consists of dissolved ions, proteins, and other small molecules. • Ions dissolved in the cytosol include K+, Na+, Cl-, Mg2+, Ca2+, and bicarbonate. It also contains amino acids, proteins, and molecules that regulate osmolarity, such as protein kinase C and calmodulin. • Membrane-bound organelles: • Nucleus: The control center of the cell, containing the genetic material (DNA).  • Mitochondria: The powerhouses of the cell, responsible for generating energy through cellular respiration.  • Endoplasmic reticulum (ER): A network of membranes involved in protein and lipid synthesis, folding, and transport.  • Golgi apparatus: Modifies, sorts, and packages proteins and other molecules for transport within or outside the cell.  • Lysosomes: Contain enzymes that break down cellular waste and debris.  • Vacuoles: Store water, nutrients, and waste products.  • Non-membrane-bound organelles: • Ribosomes: Sites of protein synthesis.  • Cytoskeleton: Provides structural support and enables movement within the cell.  • Other structures: • Cell membrane: The outer boundary of the cell, regulating the entry and exit of materials.  • Cell wall (in plant cells): Provides support and protection to the cell.  • Chloroplasts (in plant cells): Sites of photosynthesis, converting light energy into chemical energy.  • Cytoplasmic inclusions are non-living, temporary structures within the cytoplasm that accumulate stored nutrients, secretory products, or pigment granules. • 3 Main Cytoplasmic Inclusions : • Glycogen granules : These are the storage form of glucose and are particularly abundant in liver and muscle cells. • Lipid droplets : These are spherical structures containing accumulated triglycerides and are found in various tissues, especially fat cells. • Pigments : These are colored substances that can be found in various cells, such as melanin in skin and hair cells.

Introduction • The plasma membrane, also known as the cell membrane, is a semipermeable membrane that surrounds all cells, separating the interior of the cell from the external environment. • Sure! Here are the 3 functions without explanation: 1. Selective permeability 2. Cell communication and signaling 3. Structural support and protection • The requisite barrier is provided by the plasma membrane, which forms the cell’s outer skin. Structure • 5 Main parts of Plasma Membrane : 1. 1. Phospholipid Bilayer: This is the primary structural component of the membrane, forming a double layer with hydrophobic fatty acid tails facing inward and hydrophilic phosphate heads facing outward.  2. 2. Integral Proteins: These proteins are embedded within the phospholipid bilayer and can span the entire membrane, acting as channels, transporters, or receptors.  3. 3. Peripheral Proteins: These proteins are loosely attached to the inner or outer surface of the membrane and can play roles in signaling, cell adhesion, and structural support.  4. 4. Carbohydrates: These are attached to lipids (glycolipids) and proteins (glycoproteins) on the outer surface of the membrane and are involved in cell recognition and signaling.  5. 5. Cholesterol: This sterol is found in animal cell membranes and helps to regulate the fluidity and stability of the membrane.

Structure of a Cell – Extended • All living organisms are made up of cells. The structure of a cell includes several important parts, each with a specific function. Cells can be broadly classified into two types: prokaryotic and eukaryotic. • Here’s a breakdown of the structure of a typical eukaryotic cell: Cell Membrane : A thin, flexible barrier that surrounds the cell. It controls the movement of substances in and out of the cell. Cytoplasm : The jelly-like substance inside the cell where most cellular activities take place. It contains all the organelles. Nucleus : The control center of the cell. It contains DNA and manages cell activities like growth and reproduction. Mitochondria : Known as the powerhouse of the cell, mitochondria produce energy through respiration. Ribosomes : These are the sites where proteins are made. They can be found floating freely in the cytoplasm or attached to the endoplasmic reticulum. Endoplasmic Reticulum (ER) : There are two types: rough ER (with ribosomes) and smooth ER (without ribosomes). The ER helps in the transport of materials and production of proteins and lipids. Golgi Apparatus : It modifies, sorts, and packages proteins and lipids for storage or transport out of the cell. Lysosomes : These contain enzymes that break down waste materials and cellular debris. Vacuoles : Storage structures that hold food, water, and waste. Plant cells usually have one large vacuole, while animal cells have smaller ones. Cell Wall : (only in plant cells)A rigid outer layer that provides support and protection. Chloroplasts (only in plant cells) : These contain chlorophyll and are responsible for photosynthesis, allowing plants to make their own food. • The structure of a cell is highly organized, and each part plays a vital role in keeping the cell—and the organism—alive and functioning.

Blood vascular endothelial cells • Endothelial cells (ECs) form a single cell layer that lines all blood vessels. Tumor ECs display a remarkable heterogeneity and plasticity, and they control the passage of proteins, cells, oxygen, and fluid into the surrounding tissue. • ECs that line tumor blood vessels differ from normal ECs. Tumor ECs express lower levels of adhesion molecules, which causes an impaired barrier function, and they express increased levels of inhibitory immune checkpoint molecules, which contributes to immunosuppression. Lymphatic ECs • Lymphatic ECs (LECs) form the walls of lymphatic vessels. In the TME, lymphatic vessels provide a dissemination route for cancer cells in addition to blood vessels. • LECs have recently also been recognized as direct regulators of anti-tumor immunity and immunotherapy response. LECs can present tumor antigens but also immune checkpoint molecules. Ma et al.348 Pericytes • Pericytes, also known as mural cells, surround blood vessels and are embedded in the basement membrane of vessels and adjacent to ECs. They support the maturation and permeability of the vasculature. • In tumors, an impaired interaction between pericytes and ECs contributes to a leaky and dysfunctional tumor vasculature. • Pericytes also interact with other stromal cells and cancer cells via paracrine mechanisms, resulting in modulation of the TME. In particular, there is growing interest in the immunomodulatory activity of pericytes.

Cancer-associated fibroblasts • Cancer-associated fibroblasts (CAFs) are a key component of the tumor stroma. CAFs are composed of multiple functionally distinct subtypes that display an enormous plasticity. CAFs exert pleiotropic and opposing functions within the TME. • CAFs synthesize and remodel the ECM, which changes the mechanical properties of the ECM and alters the behavior of cancer cells and immune cells. CAFs impact angiogenesis, and they have a strong immunomodulatory capacity and contribute to immune evasion of cancer. ECM • The ECM is a non-cellular structural component of the TME and comprises a network of fibrous proteins, such as collagens, glycoproteins, and proteoglycans. The ECM is a dynamic structure that is continuously remodeled by proteases produced by a variety of cells in the TME. The composition of matrisomal proteins in the ECM varies between tumor types and stages. • The ECM facilitates intercellular communication in the TME by acting as a reservoir for the sequestration of secreted molecules and as a substrate for cell adhesion and migration. • ECM remodeling by proteases liberates tethered molecules, thus generating localized high concentrations of released mediators. Cancer and TME cells directly contact the surrounding ECM via receptors including integrins and CD44, which form part of the diverse signaling networks that are activated in cancer. Adipocytes • Adipocytes are present in numerous tissues, and they are specialized in storing energy as fat. Obesity is a key risk factor for multiple cancer types. Cancer-associated adipocytes are emerging key contributors to cancer types. • They release free fatty acids, hormones, cytokines, adipokines, and growth factors that impact cancer cells as well as host cells in the TME. There is active interchange of metabolites and amino acids between adipocytes and cancer cells. • Cancer-associated adipocytes have strong immunoregulatory capacity. They contribute to pro-tumorigenic low-grade chronic inflammation by producing chemoattractants for myeloid cells. Neurons and nerves • Neurons and nerve fibers are present in the TME. Accumulating evidence demonstrates that neurons contribute to tumorigenesis. Perineural invasion (PNI) is a process by which cancer cells locally extend along nerves, which is observed in several solid cancer types and is associated with poor outcomes. • Moreover, there is active crosstalk between neurons and cancer cells in the TME via reciprocal paracrine signaling. • Neurons release neurotransmitters, neurotrophins, and chemokines, which stimulate cancer stemness, resistance to apoptosis, and enhanced proliferation. Moreover, nerves regulate inflammation and immune response in the TME, in the central nervous system, and in extracranial organs and is an active field of cancer research.

Adaptive immune cells CD8+ T cells : CD8+ T cells are powerful effector cells in the anti-tumor immune response. CD8+ T cells can specifically recognize cancer cells by binding with their T cell receptor (TCR) to MHC-peptide complexes expressed by cancer cells. Upon TCR engagement, CD8+ T cells destroy target cells through granzyme and perforin-mediated apoptosis or via FASL-FAS-mediated cell death. In tumors, many different CD8+ T cell states can be found. Often, intratumoral CD8+ T cells have a dysfunctional or exhausted phenotype. Immune checkpoint blockade aims to unleash CD8+ T cell responses against cancer.Philip and Schietinger. CD4+ T cells : CD4+ helper T cells influence a variety of other immune cells; in particular, they contribute to effective CD8+ T cell responses. In cancer, CD4+ T cells play a dual role. In particular, the Th1 subtype of CD4+ T cells exerts anti-tumorigenic functions by providing help to anti-tumor cytotoxic CD8+ cells and B cells and by direct killing of cancer cells via the production of interferon γ (IFNγ) and TNF-α. On the other hand, the Th2 subtype secretes anti-inflammatory mediators that exert pro-tumoral functions. There is growing evidence that CD4+ T cells may play important roles in efficacy of immune checkpoint blockade (ICB).DeNardo et al. Tregs : Regulatory T cells (Tregs) are a highly immunosuppressive subset of CD4+ T cells and function as gatekeepers of immune homeostasis. Tregs can be subdivided into thymic-derived and peripherally induced Tregs. In cancer, Tregs suppress effective anti-tumor immunity through different mechanisms. Their exact effector program is dependent on context-dependent cues. Treg-targeted cancer therapies are under investigation but are challenging given the key role of Tregs in preventing autoimmunity. B cells : B lymphocytes are key mediators of humoral immunity. In cancer, B cells can exert anti-tumor effects through antibody-dependent cell cytotoxicity and complement activation. B cells can reside in intratumoral tertiary lymphoid structures (TLSs), where they contribute to T cell activation via antigen presentation. B cells can also support tumor growth by promoting inflammation and immunosuppression via secretion of anti-inflammatory and pro-angiogenic mediators, via immune-complexes, and via complement activation. A subpopulation of immunosuppressive B cells, Bregs, are involved in immunological tolerance.Yuen et al. Myeloid immune cells Macrophages : Tumor-associated macrophages (TAMs) represent a highly plastic immune cell population with both pro- and anti-tumorigenic functions. TAMs comprise multiple subsets that arise from different origins (yolk sac-derived tissue-resident macrophages or bone marrow-derived infiltrating macrophages). Moreover, multiple TAM subsets co-exist in tumors. Pro-tumorigenic functions of TAMs include promoting angiogenesis, immunosuppression, metastasis formation, and therapy resistance, while TAMs can also counteract cancer progression by direct phagocytosis of cancer cells or activation of anti-tumor immune responses. Neutrophils : Neutrophils are the most abundant immune cells in blood. Besides their recruitment to primary tumors, neutrophils frequently accumulate in blood and distant organs of tumor-bearing hosts. Depending on cues from the TME and their maturation status, neutrophils can exert anti- or pro-tumorigenic functions. Their systemic accumulation contributes to immunosuppression and extracellular matrix (ECM) remodeling in distant organs, which promote (pre)metastatic niche formation. Neutrophil diversity and plasticity in cancer is a topic of intense investigation. Monocytes : Monocytes circulate in the bloodstream and migrate into tissues where they differentiate into macrophages and dendritic cells (DCs). Several subtypes of monocytes exist, including classical, non-classical, and intermediate monocytes. Recent single-cell RNA sequencing studies demonstrated additional monocyte subpopulations. In cancer, monocytes exert pro- and anti-tumoral functions. Monocytes can produce tumoricidal mediators and stimulate natural killer (NK) cells. However, in the TME, they contribute to immunosuppression, ECM remodeling, angiogenesis, and cancer cell intravasation. Moreover, they differentiate into tumor-supporting TAMs. DCs : DCs are a diverse group of antigen-presenting cells critical for initiating and regulating adaptive immune responses. By integrating information from the TME and relaying it to other immune cells, most notably T cells, DCs have the potential to shape anti-tumor immunity. However, tumors, in turn, employ a variety of strategies to limit and manipulate DC activity to evade immune control. Harnessing the power of DCs to improve immunotherapy response and the development of DC-based vaccines is an active field of cancer research. Mast cells : Mast cells are granulocytes that mediate host defense and maintenance of homeostasis by swiftly degranulating histamines, cytokines, and chemokines. They are well known for their role in allergies and autoimmunity, but they can also infiltrate tumors. Mast cells exert both pro- and anti-tumorigenic activities depending on the microenvironmental stimuli. They can directly target tumor cells, but they mainly regulate the recruitment and activity of other immune populations and the endothelium. Eosinophils : Eosinophils are known for their role in allergic diseases and parasite infections. More recently, their function in the TME is becoming apparent. Eosinophils have the capacity to directly kill tumor cells via the release of cytotoxic molecules, but eosinophils can also modulate the tumor vasculature and regulate the immune composition of the TME, and as such, they can have both pro- and anti-tumorigenic functions depending on the activation signals they receive. In addition, there is a growing interest in the role of eosinophils in promoting immunotherapy response. Myeloid-derived suppressor cells : Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of myeloid cells, consisting of (immature) monocytic and neutrophilic cells with potent immunosuppressive capacities. These cells expand in patients with cancer and mouse cancer tumor models, and their presence in the TME is associated with poor clinical outcome. MDSCs suppress T cells, NK cells, B cells, and DCs via paracrine and cell-cell contact mechanisms. Platelets : Platelets, also named thrombocytes, are fragments of cytoplasm derived from megakaryocytes in the bone marrow. Platelets lack a nucleus, are abundant in blood, and are essential for blood clotting. Platelets promote tumor progression and metastasis through a range of different mechanisms. They bind to circulating tumor cells (CTCs), promoting CTC survival by shielding them from physical stress and immune attack. Platelets also release pro- and anti-angiogenic mediators, and they bind to endothelial cells, through which they modulate angiogenesis and vascular integrity. Platelets contribute to tumor-associated inflammation and immune evasion by activating myeloid cells. NK cells : NK cells are cytotoxic innate lymphoid cells. They recognize and kill stressed cells that lack MHC class I expression. Circulating and intratumoral NK cell levels are predictive for improved survival in patients with cancer. NK cells have potent anti-cancer abilities; however, progressing tumors evade elimination by NK cells via several mechanisms, such as the upregulation of inhibitory receptors that diminish NK cell cytotoxicity and the mobilization of immunosuppressive myeloid cells and Tregs. There is a growing interest in utilizing NK cells in the next generation of immunotherapeutic modalities either by engaging endogenous NK cells or by NK cell-based cellular therapies. Invariant NK T cellsIn : variant NK T (iNKT) cells are CD1d-restricted lipid-specific T lymphocytes that bridge innate and adaptive immunity and can mediate a plethora of immune functions depending on tissue distribution. In several experimental models, iNKT cells exert cancer immunosurveillance through direct tumor cell killing or by orchestrating the activity of both pro- or anti-tumorigenic immune cells. Cancer-associated immunosuppression can skew iNKT cell activity toward more regulatory functions. Gamma delta T cells : Gamma delta (γδ) T cells form an unconventional T cell population expressing yδ TCRs, but not αβ TCRs, that recognize target antigens in an MHC-independent manner. Depending on the subset, yδ T cells exert effector or regulatory functions. In cancer, yδ T cells may promote disease progression by suppressing anti-tumor immune responses via the production of cytokines, including IL-17. Anti-tumor immunity can also be induced by yδ T cells via direct cytotoxicity mediated by TCR- or NK-receptor interactions or production of effector molecules. Innate-like lymphocytes : Innate-like lymphocytes (ILCs) are a highly diverse group of immune cells that reside in tissues and that function at the intersection of adaptive and innate immunity. Besides NK cells, ILCs include ILC1s, ILC2s, and ILC3s. ILCs lack antigen-specific receptors and exert their immunoregulatory functions through secretion of a diverse array of cytokines and other inflammatory mediators. In cancer, ILCs play opposing roles. Depending on the tumor types and on cues from the TME, a different composition and activation phenotype of ILC subsets can be found in human tumors. Our understanding of the roles of the different ILCs subtypes in cancer is still very limited.

Cancer, It's striking how from just a genetic disease that was accountable for about 2.35% of death in 1954 (First year Cancer was recognised), to a very complex disease almost accountable for 16.8% of death in 2024. It has let it's leash into the attention of the researches : A 2023 analysis by the National Institutes of Health (NIH) found 7747 clinical trials focused on cancer. Furthermore, The Lancet reported 66,388 awards for cancer research between 2016 and 2020, totaling $24.5 billion. The intricate complexity of cancer becomes evident upon microscopic examination of solid tumors, revealing that the tumor microenvironment (TME) is a highly structured ecosystem containing cancer cells surrounded by diverse non-malignant cell types, collectively embedded in an altered, vascularized extracellular matrix (Figure 1). The TME includes a rich diversity of immune cells, cancer-associated fibroblasts (CAFs), endothelial cells (ECs), pericytes, and other cell types that vary by tissue—such as adipocytes and neurons.

Ch : 5 States of Matter Pages No. 68,69 Introduction • The three states of matter are solid, liquid, and gas. Examples of each state include:  • Solids: Ice, wood, stone, iron, bricks, paper, concrete, glass, dry ice, salt, and most metals and minerals  • Liquids: Water, milk, juice, oil, alcohol, and mercury  • Gases: Air, helium, hydrogen, oxygen, nitrogen, carbon dioxide, and natural gas  • The state of matter depends on how the particles are arranged and how much energy they have. Solids  • Have a definite shape and volume • Particles are closely packed together and vibrate in place Liquids  • Have a definite volume but can change shape • Particles are loosely bonded and move around but stay close together • Take the shape of their container Gases  • Have neither a definite shape nor volume • Particles move freely and spread apart from one another • Fill their container, taking both the shape and the volume of the container

What is Primed Pluripotency? • Primed pluripotency is a state of stem cells that are still pluripotent, meaning they can form any of the three germ layers: • Ectoderm (e.g., brain, skin) • Mesoderm (e.g., heart, blood, muscle) • Endoderm (e.g., gut, liver, lungs) • However, primed cells are not as flexible as naive pluripotent cells. • They are “primed” or ready to begin differentiating, meaning they are closer to becoming specific cell types. Origin in the Embryo • Primed pluripotent cells exist in the epiblast of the post-implantation embryo, which forms after the embryo attaches to the uterus. • These cells are more developmentally advanced than naive cells (which come from the earlier, pre-implantation embryo). Laboratory Examples • Mouse Epiblast Stem Cells (EpiSCs): • Derived from post-implantation mouse embryos. • Serve as the mouse model for primed pluripotency. • Human Embryonic Stem Cells (hESCs): • Most hESCs cultured in labs naturally exist in the primed state, unless specially converted to naive. Molecular and Epigenetic Features • Epigenetic State: • DNA is more methylated, meaning genes are less accessible for activation. • Chromatin (DNA + protein) is more compact, indicating partial gene silencing. • X-Chromosome Inactivation (Females Only): • One of the two X chromosomes is already inactivated, which happens in more differentiated cells. • This is different from naive cells, which have both X chromosomes active. • Transcription Factors: • Express some core pluripotency factors like OCT4, SOX2, NANOG, but at different levels than in naive cells. • Additional factors like OTX2 are often upregulated, which helps push the cells toward differentiation. Molecular and Epigenetic Features • Epigenetic State: • DNA is more methylated, meaning genes are less accessible for activation. • Chromatin (DNA + protein) is more compact, indicating partial gene silencing. • X-Chromosome Inactivation (Females Only): • One of the two X chromosomes is already inactivated, which happens in more differentiated cells. • This is different from naive cells, which have both X chromosomes active. • Transcription Factors: • Express some core pluripotency factors like OCT4, SOX2, NANOG, but at different levels than in naive cells. • Additional factors like OTX2 are often upregulated, which helps push the cells toward differentiation. Growth Requirements and Signaling • Primed cells need specific growth factors to survive and stay pluripotent in culture: • FGF2 (Fibroblast Growth Factor 2) – essential for cell survival and proliferation. • Activin A/Nodal signaling – keeps the cells in the pluripotent state. • If these signals are removed, the cells will start differentiating into specific cell types. Metabolism and Energy Usage • Primed cells rely more on glycolysis for energy (breaking down glucose in the cytoplasm). • Naive cells rely more on oxidative phosphorylation in the mitochondria. • This metabolic shift reflects their transition toward more active, specialized cells. Behavior in Experiments • Chimera Formation: • When injected into an early embryo, primed cells do not efficiently integrate into the developing organism. • Naive cells, by contrast, can integrate well and form all tissues, even contribute to the germline. • Colony Morphology (in dishes): • Primed cells grow in flat, spread-out colonies. • Naive cells grow in tight, dome-shaped colonies. Conceptual Analogy • Imagine pluripotency like a student’s academic journey: • Naive pluripotent cell = a student in elementary school with no set path—can become anything. • Primed pluripotent cell = a high school senior who's chosen a general field (like science or arts), but hasn't picked a specific job yet—options are still open, but more limited.

• Naïve pluripotency is the earliest and most flexible state that a pluripotent stem cell can be in. It represents cells from the inner cell mass of a very early embryo (before it implants in the uterus). These cells can become any cell type in the body, and they are not yet limited in their potential. Where Do Naïve Cells Come From? • They come from the pre-implantation embryo (around day 3–4 in mice). • In the lab, these cells are called naïve embryonic stem cells (ESCs) and are usually studied in mice. • Human ESCs are usually in a slightly later state called primed, but scientists can also create naïve-like human stem cells using special methods. What Makes Naïve Stem Cells Special? • Very flexible: Can turn into any cell type in the body. • Grow well: Can divide many times without changing or aging. • Simple DNA state: • Low DNA methylation (the DNA is more “open” and active). • In females, both X chromosomes are active, unlike in most cells. • Key genes turned on: • OCT4, SOX2, NANOG, KLF4, and others — these help keep the cell in its pluripotent state. How Are Naïve Cells Grown in the Lab? Scientists use special culture conditions called "2i + LIF": • 2i = two chemicals that block signals pushing the cell to differentiate (PD0325901 and CHIR99021). • LIF = a protein that helps the cell stay pluripotent. These conditions keep the cells in their naïve state — like freezing them at their most flexible moment. Why Is Naïve Pluripotency Important? • Better understanding of early development. • More efficient cell reprogramming (turning adult cells back into stem cells). • Useful in genetic editing and research. • Potential for future regenerative medicine — building organs, repairing tissues, etc. Summary • Naïve pluripotency is like the “blankest” state a stem cell can be in — full of potential, not yet committed, and easy to guide into becoming any type of cell. Understanding this state helps scientists learn how life begins and how to use stem cells in medicine.